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487  structures 1793  species 0  interactions 17289  sequences 159  architectures

Family: Serpin (PF00079)

Summary: Serpin (serine protease inhibitor)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Serpin". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Serpin (serine protease inhibitor) Provide feedback

Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.

Literature references

  1. Wright HT; , Bioessays 1996;18:453-464.: The structural puzzle of how serpin serine proteinase inhibitors work. PUBMED:8787534 EPMC:8787534


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023796

Serpins (SERine Proteinase INhibitors) belong to MEROPS inhibitor family I4, clan ID. Most serpin family members are indeed serine protease inhibitors, but several have additional cross-class inhibition functions and inhibit cysteine protease family members such as the caspases and cathepsins [ PUBMED:8034697 , PUBMED:7851535 ]. Others, such as ovalbumin, are incapable of protease inhibition and serve other functions [ PUBMED:8417965 ].

Serpins share a highly conserved core structure that is critical for their functioning as serine protease inhibitors [ PUBMED:21781239 ]. Inhibitory serpins comprise several alpha-helix and beta-strands together with an external reactive centre loop (RCL) containing the active site recognised by the target enzyme. Serpins form covalent complexes with target proteases. Their mechanism of protease inhibition is known as irreversible "trapping" , in which a rapid conformational change traps the cognate protease in a covalent complex.

This entry represents the structural domain of serpins.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(115)
Full
(17289)
Representative proteomes UniProt
(35751)
RP15
(3322)
RP35
(7930)
RP55
(15203)
RP75
(20087)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(115)
Full
(17289)
Representative proteomes UniProt
(35751)
RP15
(3322)
RP35
(7930)
RP55
(15203)
RP75
(20087)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(115)
Full
(17289)
Representative proteomes UniProt
(35751)
RP15
(3322)
RP35
(7930)
RP55
(15203)
RP75
(20087)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Overington and HMM_iterative_training
Previous IDs: serpin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Eddy SR
Number in seed: 115
Number in full: 17289
Average length of the domain: 294.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 84.30 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 370
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Serpin domain has been found. There are 487 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JSK1 View 3D Structure Click here
A0A0G2L1U5 View 3D Structure Click here
A0A0N7KSP2 View 3D Structure Click here
A0A0P0VRG4 View 3D Structure Click here
A0A0P0WCS7 View 3D Structure Click here
A0A0P0WPC8 View 3D Structure Click here
A0A0P0Y0C9 View 3D Structure Click here
A0A0P0Y0W3 View 3D Structure Click here
A0A0R4IY13 View 3D Structure Click here
A0A1D6GLS4 View 3D Structure Click here
A0A1D6GLS4 View 3D Structure Click here
A0A1D6MQ86 View 3D Structure Click here
A0A1D6MQ86 View 3D Structure Click here
A0A1P8ANB3 View 3D Structure Click here
A0A1P8ANB3 View 3D Structure Click here
A0A2R8PXE0 View 3D Structure Click here
A0A2R8PZC2 View 3D Structure Click here
A0A2R8QA46 View 3D Structure Click here
A0A2R8QCZ5 View 3D Structure Click here
A1Z6I3 View 3D Structure Click here
A1Z6R3 View 3D Structure Click here
A1Z6R4 View 3D Structure Click here
A1Z6V5 View 3D Structure Click here
A2RSF9 View 3D Structure Click here
A8KBW0 View 3D Structure Click here
A8MTL9 View 3D Structure Click here
A8MV23 View 3D Structure Click here
A8WFU6 View 3D Structure Click here
A9Z1L1 View 3D Structure Click here
B0UYL8 View 3D Structure Click here
B0V2R7 View 3D Structure Click here
B0V3R7 View 3D Structure Click here
B3DJI9 View 3D Structure Click here
B4FT53 View 3D Structure Click here
B6TJI3 View 3D Structure Click here
D3Z450 View 3D Structure Click here
D3Z451 View 3D Structure Click here
D3Z660 View 3D Structure Click here
D3ZAT4 View 3D Structure Click here
D3ZHB5 View 3D Structure Click here
D3ZJI7 View 3D Structure Click here
D3ZJK2 View 3D Structure Click here
D3ZKA0 View 3D Structure Click here
D3ZN36 View 3D Structure Click here
D3ZPF9 View 3D Structure Click here
D4A392 View 3D Structure Click here
D4A4R7 View 3D Structure Click here
D4A4U8 View 3D Structure Click here
D4A9F7 View 3D Structure Click here
E7EXC4 View 3D Structure Click here
E9Q6A2 View 3D Structure Click here
F1M8F5 View 3D Structure Click here
F1MAA9 View 3D Structure Click here
F1MAA9 View 3D Structure Click here
F1QHG3 View 3D Structure Click here
F1QQ04 View 3D Structure Click here
F1QQ30 View 3D Structure Click here
F1QRB8 View 3D Structure Click here
F1R9A9 View 3D Structure Click here
F1RAP6 View 3D Structure Click here
F4HX47 View 3D Structure Click here
F4I826 View 3D Structure Click here
F6NQ58 View 3D Structure Click here
F6V5V4 View 3D Structure Click here
F7EMJ6 View 3D Structure Click here
F7F6T5 View 3D Structure Click here
F7FHF3 View 3D Structure Click here
F8W298 View 3D Structure Click here
F8W3S9 View 3D Structure Click here
F8W475 View 3D Structure Click here
F8W5D3 View 3D Structure Click here
F8WGA3 View 3D Structure Click here
G3V6B5 View 3D Structure Click here
G3V7A3 View 3D Structure Click here
G3V8X9 View 3D Structure Click here
G3X9V8 View 3D Structure Click here
G5ECY2 View 3D Structure Click here
G5EE40 View 3D Structure Click here
G5EFH4 View 3D Structure Click here
I1JTG3 View 3D Structure Click here
I1K7W5 View 3D Structure Click here
I7HJI3 View 3D Structure Click here
I7HJI5 View 3D Structure Click here
M0R455 View 3D Structure Click here
M0RE01 View 3D Structure Click here
O04582 View 3D Structure Click here
O04582 View 3D Structure Click here
O08797 View 3D Structure Click here
O08800 View 3D Structure Click here
O08804 View 3D Structure Click here
O08806 View 3D Structure Click here
O17365 View 3D Structure Click here
O18231 View 3D Structure Click here
O35684 View 3D Structure Click here
O48706 View 3D Structure Click here
O62309 View 3D Structure Click here
O75635 View 3D Structure Click here
O75830 View 3D Structure Click here
O82283 View 3D Structure Click here
P01008 View 3D Structure Click here
P01009 View 3D Structure Click here
P01011 View 3D Structure Click here
P01015 View 3D Structure Click here
P01019 View 3D Structure Click here
P05120 View 3D Structure Click here
P05121 View 3D Structure Click here
P05154 View 3D Structure Click here
P05155 View 3D Structure Click here
P05543 View 3D Structure Click here
P05544 View 3D Structure Click here
P05545 View 3D Structure Click here
P05546 View 3D Structure Click here
P07092 View 3D Structure Click here
P07093 View 3D Structure Click here
P07758 View 3D Structure Click here
P07759 View 3D Structure Click here
P08185 View 3D Structure Click here
P08697 View 3D Structure Click here
P09005 View 3D Structure Click here
P09006 View 3D Structure Click here
P11859 View 3D Structure Click here
P12388 View 3D Structure Click here
P17475 View 3D Structure Click here
P19324 View 3D Structure Click here
P20848 View 3D Structure Click here
P20961 View 3D Structure Click here
P22599 View 3D Structure Click here
P22777 View 3D Structure Click here
P29457 View 3D Structure Click here
P29508 View 3D Structure Click here
P29524 View 3D Structure Click here
P29621 View 3D Structure Click here
P29622 View 3D Structure Click here
P30740 View 3D Structure Click here
P31211 View 3D Structure Click here
P32261 View 3D Structure Click here
P35237 View 3D Structure Click here
P35577 View 3D Structure Click here
P36952 View 3D Structure Click here
P36955 View 3D Structure Click here
P48594 View 3D Structure Click here
P48595 View 3D Structure Click here
P49182 View 3D Structure Click here
P50452 View 3D Structure Click here
P50453 View 3D Structure Click here
P50454 View 3D Structure Click here
P61939 View 3D Structure Click here
P70124 View 3D Structure Click here
P70458 View 3D Structure Click here
P70564 View 3D Structure Click here
P97290 View 3D Structure Click here
P97298 View 3D Structure Click here
Q00896 View 3D Structure Click here
Q00897 View 3D Structure Click here
Q00898 View 3D Structure Click here
Q03734 View 3D Structure Click here
Q06770 View 3D Structure Click here
Q07235 View 3D Structure Click here
Q0DQC3 View 3D Structure Click here
Q0E8C8 View 3D Structure Click here
Q0E8V6 View 3D Structure Click here
Q10GX0 View 3D Structure Click here
Q18287 View 3D Structure Click here
Q19651 View 3D Structure Click here
Q2R8P2 View 3D Structure Click here
Q3HKQ3 View 3D Structure Click here
Q3UWK8 View 3D Structure Click here
Q4G075 View 3D Structure Click here
Q4PSX8 View 3D Structure Click here
Q4V3G2 View 3D Structure Click here
Q53KS8 View 3D Structure Click here
Q53KS9 View 3D Structure Click here
Q53MD1 View 3D Structure Click here
Q53MD3 View 3D Structure Click here
Q53P09 View 3D Structure Click here
Q53Q27 View 3D Structure Click here
Q53Q31 View 3D Structure Click here
Q53Q32 View 3D Structure Click here
Q5I2A0 View 3D Structure Click here
Q5M7T5 View 3D Structure Click here
Q5M8C3 View 3D Structure Click here
Q5NBM0 View 3D Structure Click here
Q5RIH8 View 3D Structure Click here
Q5RIK7 View 3D Structure Click here
Q5SPJ1 View 3D Structure Click here
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Q5SV42 View 3D Structure Click here
Q60854 View 3D Structure Click here
Q61247 View 3D Structure Click here
Q62975 View 3D Structure Click here
Q63556 View 3D Structure Click here
Q64268 View 3D Structure Click here
Q66I20 View 3D Structure Click here
Q6AYF8 View 3D Structure Click here
Q6DG30 View 3D Structure Click here
Q6P4P1 View 3D Structure Click here
Q6P734 View 3D Structure Click here
Q6P9U0 View 3D Structure Click here
Q6UKZ0 View 3D Structure Click here
Q6UXR4 View 3D Structure Click here
Q6UXR4 View 3D Structure Click here
Q75H81 View 3D Structure Click here
Q7JV69 View 3D Structure Click here
Q7JWX3 View 3D Structure Click here
Q7K508 View 3D Structure Click here
Q7K8Y5 View 3D Structure Click here
Q7KA66 View 3D Structure Click here
Q7T309 View 3D Structure Click here
Q7TMF5 View 3D Structure Click here
Q7TPA5 View 3D Structure Click here
Q7XMK0 View 3D Structure Click here
Q7XMK0 View 3D Structure Click here
Q7XMK1 View 3D Structure Click here
Q7YTY6 View 3D Structure Click here
Q7ZVL5 View 3D Structure Click here
Q80UK5 View 3D Structure Click here
Q80X76 View 3D Structure Click here
Q80ZA3 View 3D Structure Click here
Q86U17 View 3D Structure Click here
Q86WD7 View 3D Structure Click here
Q8AYE3 View 3D Structure Click here
Q8BMT0 View 3D Structure Click here
Q8BYY9 View 3D Structure Click here
Q8CDC0 View 3D Structure Click here
Q8CIE0 View 3D Structure Click here
Q8IW75 View 3D Structure Click here
Q8JH29 View 3D Structure Click here
Q8K1K6 View 3D Structure Click here
Q8K3K4 View 3D Structure Click here
Q8R121 View 3D Structure Click here
Q8R4Z1 View 3D Structure Click here
Q8SYY7 View 3D Structure Click here
Q8SZF4 View 3D Structure Click here
Q8VHP7 View 3D Structure Click here
Q8VHQ1 View 3D Structure Click here
Q91WP6 View 3D Structure Click here
Q94DW6 View 3D Structure Click here
Q96P15 View 3D Structure Click here
Q96P63 View 3D Structure Click here
Q99574 View 3D Structure Click here
Q9C8T2 View 3D Structure Click here
Q9CQV3 View 3D Structure Click here
Q9D154 View 3D Structure Click here
Q9D1Q5 View 3D Structure Click here
Q9D695 View 3D Structure Click here
Q9D7D2 View 3D Structure Click here
Q9D7P9 View 3D Structure Click here
Q9DAV6 View 3D Structure Click here
Q9DCQ7 View 3D Structure Click here
Q9JK88 View 3D Structure Click here
Q9JLD2 View 3D Structure Click here
Q9M1T7 View 3D Structure Click here
Q9S7T8 View 3D Structure Click here
Q9SH52 View 3D Structure Click here
Q9SH52 View 3D Structure Click here
Q9SIR9 View 3D Structure Click here
Q9UIV8 View 3D Structure Click here
Q9UK55 View 3D Structure Click here
Q9V3N1 View 3D Structure Click here
Q9VA48 View 3D Structure Click here
Q9VA48 View 3D Structure Click here
Q9VFC1 View 3D Structure Click here
Q9VFC2 View 3D Structure Click here
Q9VH46 View 3D Structure Click here
Q9VH46 View 3D Structure Click here
Q9VII7 View 3D Structure Click here
Q9VL44 View 3D Structure Click here
Q9VLQ7 View 3D Structure Click here
Q9VLU4 View 3D Structure Click here
Q9VLV3 View 3D Structure Click here
Q9VLZ8 View 3D Structure Click here
Q9VPH9 View 3D Structure Click here
Q9VVW1 View 3D Structure Click here
Q9VWB4 View 3D Structure Click here
Q9XUS1 View 3D Structure Click here
Q9XVQ1 View 3D Structure Click here
Q9ZQR6 View 3D Structure Click here
Q9ZQR6 View 3D Structure Click here
W4VSP4 View 3D Structure Click here