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108  structures 4033  species 0  interactions 20489  sequences 510  architectures

Family: OB_NTP_bind (PF07717)

Summary: Oligonucleotide/oligosaccharide-binding (OB)-fold

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Oligonucleotide/oligosaccharide-binding (OB)-fold Provide feedback

This family is found towards the C-terminus of the DEAD-box helicases (PF00270). In these helicases it is apparently always found in association with PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Q84VZ2. The structure PDB:3i4u adopts an OB-fold. helicases (PF00270). In these helicases it is apparently always found in association with PF04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins [1].

Literature references

  1. Walbott H, Mouffok S, Capeyrou R, Lebaron S, Humbert O, van Tilbeurgh H, Henry Y, Leulliot N;, EMBO J. 2010;29:2194-2204.: Prp43p contains a processive helicase structural architecture with a specific regulatory domain. PUBMED:20512115 EPMC:20512115

  2. Kim T, Pazhoor S, Bao M, Zhang Z, Hanabuchi S, Facchinetti V, Bover L, Plumas J, Chaperot L, Qin J, Liu YJ;, Proc Natl Acad Sci U S A. 2010; [Epub ahead of print]: Aspartate-glutamate-alanine-histidine box motif (DEAH)/RNA helicase A helicases sense microbial DNA in human plasmacytoid dendritic cells. PUBMED:20696886 EPMC:20696886


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011709

This domain is found towards the C terminus of the DEAD-box helicases ( INTERPRO ). In these helicases it appears to be always found in association with INTERPRO .

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
(58)
Full
(20489)
Representative proteomes UniProt
(46269)
RP15
(3397)
RP35
(9085)
RP55
(16996)
RP75
(24289)
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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
(58)
Full
(20489)
Representative proteomes UniProt
(46269)
RP15
(3397)
RP35
(9085)
RP55
(16996)
RP75
(24289)
Alignment:
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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
(58)
Full
(20489)
Representative proteomes UniProt
(46269)
RP15
(3397)
RP35
(9085)
RP55
(16996)
RP75
(24289)
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: Yeats C
Previous IDs: DUF1605;
Type: Domain
Sequence Ontology: SO:0000417
Author: Yeats C
Number in seed: 58
Number in full: 20489
Average length of the domain: 84.40 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 8.09 %

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 29.5 29.5
Trusted cut-off 29.5 29.5
Noise cut-off 29.4 29.4
Model length: 83
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Selections

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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 OB_NTP_bind domain has been found. There are 108 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
A0A0G2JTM6 View 3D Structure Click here
A0A0G2JZH9 View 3D Structure Click here
A0A0G2K1F5 View 3D Structure Click here
A0A0G2K283 View 3D Structure Click here
A0A0G2KB03 View 3D Structure Click here
A0A0G2KIQ1 View 3D Structure Click here
A0A0P0UXU4 View 3D Structure Click here
A0A0P0W309 View 3D Structure Click here
A0A0P0X951 View 3D Structure Click here
A0A0P0XV93 View 3D Structure Click here
A0A0R0ETU0 View 3D Structure Click here
A0A0R0F600 View 3D Structure Click here
A0A0R0G3M6 View 3D Structure Click here
A0A0R0GFB1 View 3D Structure Click here
A0A0R0H501 View 3D Structure Click here
A0A0R0HZN5 View 3D Structure Click here
A0A0R0K5K3 View 3D Structure Click here
A0A0R4IS12 View 3D Structure Click here
A0A1D6EAL8 View 3D Structure Click here
A0A1D6EWN6 View 3D Structure Click here
A0A1D6G548 View 3D Structure Click here
A0A1D6GAN5 View 3D Structure Click here
A0A1D6H4I5 View 3D Structure Click here
A0A1D6HJM8 View 3D Structure Click here
A0A1D6IJX7 View 3D Structure Click here
A0A1D6KJR0 View 3D Structure Click here
A0A1D6KTP8 View 3D Structure Click here
A0A1D6L4C4 View 3D Structure Click here
A0A1D6MMZ3 View 3D Structure Click here
A0A1D6NU12 View 3D Structure Click here
A0A1D6PBS8 View 3D Structure Click here
A0A1D8PG31 View 3D Structure Click here
A0A1D8PP74 View 3D Structure Click here
A0A1D8PPJ3 View 3D Structure Click here
A0A1D8PS92 View 3D Structure Click here
A0A286Y8Y8 View 3D Structure Click here
A0A286YAG0 View 3D Structure Click here
A0A2R8Q3V8 View 3D Structure Click here
A0A2R8QML1 View 3D Structure Click here
A0A368UII8 View 3D Structure Click here
A0A5K1K9B8 View 3D Structure Click here
A1Z9L3 View 3D Structure Click here
A2A4P0 View 3D Structure Click here
A2ACQ1 View 3D Structure Click here
A4HTS5 View 3D Structure Click here
A4I0U7 View 3D Structure Click here
A4IA06 View 3D Structure Click here
A4IB14 View 3D Structure Click here
A4ICJ0 View 3D Structure Click here
A4IDY1 View 3D Structure Click here
B0S6Z1 View 3D Structure Click here
B2RR83 View 3D Structure Click here
B8JLP0 View 3D Structure Click here
C0P4V0 View 3D Structure Click here
D3ZD97 View 3D Structure Click here
D3ZGJ0 View 3D Structure Click here
D3ZHW0 View 3D Structure Click here
D3ZIV8 View 3D Structure Click here
D3ZSV6 View 3D Structure Click here
D4A1R0 View 3D Structure Click here
D4A2Z8 View 3D Structure Click here
D4A321 View 3D Structure Click here
D4A474 View 3D Structure Click here
D4A9D6 View 3D Structure Click here
E7F3I8 View 3D Structure Click here
E7F525 View 3D Structure Click here
E7F7R7 View 3D Structure Click here
E7F9S1 View 3D Structure Click here
E7FCG0 View 3D Structure Click here
F1QCB1 View 3D Structure Click here
F1QND0 View 3D Structure Click here
F1QU72 View 3D Structure Click here
F4HYJ7 View 3D Structure Click here
F4I9Q5 View 3D Structure Click here
F4IDQ6 View 3D Structure Click here
F4IE66 View 3D Structure Click here
F4IJV4 View 3D Structure Click here
F4ILR7 View 3D Structure Click here
F4IM84 View 3D Structure Click here
F4INY4 View 3D Structure Click here
F4JMJ3 View 3D Structure Click here
F4JRJ6 View 3D Structure Click here
F4K2E9 View 3D Structure Click here
F4KGU4 View 3D Structure Click here
G3X8X0 View 3D Structure Click here
I1J614 View 3D Structure Click here
I1J7X3 View 3D Structure Click here
I1JBE2 View 3D Structure Click here
I1JQU1 View 3D Structure Click here
I1K5G0 View 3D Structure Click here
I1KQG1 View 3D Structure Click here
I1KVZ2 View 3D Structure Click here
I1L9L1 View 3D Structure Click here
I1LNH6 View 3D Structure Click here
I1MD84 View 3D Structure Click here
I1MYP1 View 3D Structure Click here
I1NBE6 View 3D Structure Click here
I1NFR4 View 3D Structure Click here
K7K1P9 View 3D Structure Click here
K7K610 View 3D Structure Click here
K7K7U5 View 3D Structure Click here
K7KB99 View 3D Structure Click here
K7KCE6 View 3D Structure Click here
K7KW48 View 3D Structure Click here
K7L463 View 3D Structure Click here
K7LD94 View 3D Structure Click here
K7M1E8 View 3D Structure Click here
K7M4P5 View 3D Structure Click here
K7M8L9 View 3D Structure Click here
K7MP06 View 3D Structure Click here
O01598 View 3D Structure Click here
O22899 View 3D Structure Click here
O35286 View 3D Structure Click here
O42643 View 3D Structure Click here
O42945 View 3D Structure Click here
O43143 View 3D Structure Click here
O45244 View 3D Structure Click here
O46072 View 3D Structure Click here
O60114 View 3D Structure Click here
O60231 View 3D Structure Click here
O70133 View 3D Structure Click here
O94536 View 3D Structure Click here
P0CE10 View 3D Structure Click here
P15938 View 3D Structure Click here
P20095 View 3D Structure Click here
P24384 View 3D Structure Click here
P24785 View 3D Structure Click here
P34305 View 3D Structure Click here
P34498 View 3D Structure Click here
P36009 View 3D Structure Click here
P43329 View 3D Structure Click here
P53131 View 3D Structure Click here
Q03319 View 3D Structure Click here
Q04217 View 3D Structure Click here
Q06698 View 3D Structure Click here
Q08211 View 3D Structure Click here
Q09530 View 3D Structure Click here
Q0E1V1 View 3D Structure Click here
Q10752 View 3D Structure Click here
Q14147 View 3D Structure Click here
Q14562 View 3D Structure Click here
Q20644 View 3D Structure Click here
Q20875 View 3D Structure Click here
Q22307 View 3D Structure Click here
Q2R6C2 View 3D Structure Click here
Q38953 View 3D Structure Click here
Q4CP19 View 3D Structure Click here
Q4CTW3 View 3D Structure Click here
Q4CWS4 View 3D Structure Click here
Q4D1V7 View 3D Structure Click here
Q4DBT2 View 3D Structure Click here
Q4DN08 View 3D Structure Click here
Q4DW32 View 3D Structure Click here
Q4DZG3 View 3D Structure Click here
Q4E099 View 3D Structure Click here
Q4E5A4 View 3D Structure Click here
Q54F05 View 3D Structure Click here
Q54KG8 View 3D Structure Click here
Q54MH3 View 3D Structure Click here
Q54MH4 View 3D Structure Click here
Q54NJ4 View 3D Structure Click here
Q55CD3 View 3D Structure Click here
Q55EC3 View 3D Structure Click here
Q55F84 View 3D Structure Click here
Q55GT9 View 3D Structure Click here
Q5ADM3 View 3D Structure Click here
Q5AJA5 View 3D Structure Click here
Q5ANN5 View 3D Structure Click here
Q5BJS0 View 3D Structure Click here
Q5QNI3 View 3D Structure Click here
Q5XI69 View 3D Structure Click here
Q5Z9X4 View 3D Structure Click here
Q5ZAP0 View 3D Structure Click here
Q6I5X9 View 3D Structure Click here
Q6MG13 View 3D Structure Click here
Q6NZL1 View 3D Structure Click here
Q6P158 View 3D Structure Click here
Q6P5D3 View 3D Structure Click here
Q6PE54 View 3D Structure Click here
Q6PGC1 View 3D Structure Click here
Q6Z742 View 3D Structure Click here
Q7K3M5 View 3D Structure Click here
Q7L2E3 View 3D Structure Click here
Q7L7V1 View 3D Structure Click here
Q7XIR8 View 3D Structure Click here
Q7Z478 View 3D Structure Click here
Q80VY9 View 3D Structure Click here
Q80X98 View 3D Structure Click here
Q869Z1 View 3D Structure Click here
Q8BZS9 View 3D Structure Click here
Q8I2X7 View 3D Structure Click here
Q8I5A4 View 3D Structure Click here
Q8IB47 View 3D Structure Click here
Q8IJA4 View 3D Structure Click here
Q8IK86 View 3D Structure Click here
Q8IX18 View 3D Structure Click here
Q8IY37 View 3D Structure Click here
Q8SWT2 View 3D Structure Click here
Q8TE96 View 3D Structure Click here
Q8VHK9 View 3D Structure Click here
Q8VY00 View 3D Structure Click here
Q924H9 View 3D Structure Click here
Q92620 View 3D Structure Click here
Q93Y16 View 3D Structure Click here
Q99PU8 View 3D Structure Click here
Q9BKQ8 View 3D Structure Click here
Q9C6G0 View 3D Structure Click here
Q9C813 View 3D Structure Click here
Q9DBV3 View 3D Structure Click here
Q9FF84 View 3D Structure Click here
Q9H2U1 View 3D Structure Click here
Q9H5Z1 View 3D Structure Click here
Q9H6R0 View 3D Structure Click here
Q9H6S0 View 3D Structure Click here
Q9HDY4 View 3D Structure Click here
Q9HE06 View 3D Structure Click here
Q9LFR5 View 3D Structure Click here
Q9LZQ9 View 3D Structure Click here
Q9P774 View 3D Structure Click here
Q9VIZ3 View 3D Structure Click here
Q9VL25 View 3D Structure Click here
Q9VR29 View 3D Structure Click here
Q9VWI5 View 3D Structure Click here
Q9VX63 View 3D Structure Click here
Q9VY54 View 3D Structure Click here
Q9VZ55 View 3D Structure Click here
Q9W1I2 View 3D Structure Click here
U4PRA5 View 3D Structure Click here
X1WET4 View 3D Structure Click here
X1WHV8 View 3D Structure Click here