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146  structures 4686  species 0  interactions 15821  sequences 210  architectures

Family: FAD_binding_5 (PF00941)

Summary: FAD binding domain in molybdopterin dehydrogenase

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FAD binding domain in molybdopterin dehydrogenase Provide feedback

No Pfam abstract.

Literature references

  1. Dobbek H, Gremer L, Meyer O, Huber R; , Proc Natl Acad Sci U S A 1999;96:8884-8889.: Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. PUBMED:10430865 EPMC:10430865


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002346

Oxidoreductases, that also bind molybdopterin, have essentially no similarity outside this common domain. They include aldehyde oxidase ( EC ), that converts an aldehyde and water to an acid and hydrogen peroxide, and xanthine dehydrogenase ( EC ), that converts xanthine to urate. These enzymes require molybdopterin and FAD as cofactors and have and two 2FE-2S clusters. Another enzyme that contains this domain is the Pseudomonas thermocarboxydovorans carbon monoxide oxygenase.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite 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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Pfam Clan

This family is a member of clan FAD_PCMH (CL0077), which has the following description:

The FAD-binding domains contained in this family fall within the PCMH (p-cresol methyl-hydroxylase) family of FAD binding proteins as defined in [1]. In this family, the structure of the FAD binding domain is comprised of two subdomains. Both of these subdomains have an alpha-beta fold. The first subdomain is comprised of three parallel beta strands, surrounded by alpha helices. The second subdomain contains five antiparallel beta strands, also surrounded by alpha helices. The junction between these two subdomains forms the FAD bind pocket, where the ligand is bound by hydrogen and van der Waals bonds [1].

The clan contains the following 2 members:

FAD_binding_4 FAD_binding_5

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
(67)
Full
(15821)
Representative proteomes UniProt
(66057)
RP15
(1827)
RP35
(6720)
RP55
(15468)
RP75
(26640)
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
(67)
Full
(15821)
Representative proteomes UniProt
(66057)
RP15
(1827)
RP35
(6720)
RP55
(15468)
RP75
(26640)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(67)
Full
(15821)
Representative proteomes UniProt
(66057)
RP15
(1827)
RP35
(6720)
RP55
(15468)
RP75
(26640)
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: Pfam-B_1112 (release 3.0)
Previous IDs: dehydrog_molyb;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 67
Number in full: 15821
Average length of the domain: 179.00 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 30.60 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.1
Noise cut-off 26.9 26.9
Model length: 171
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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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 FAD_binding_5 domain has been found. There are 146 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
A0A0R0G5H5 View 3D Structure Click here
A0A1D6GFT6 View 3D Structure Click here
A0A1D6HSW8 View 3D Structure Click here
A0A1D6HX68 View 3D Structure Click here
A0A1D6K6B9 View 3D Structure Click here
A0A1D6L715 View 3D Structure Click here
A0A1D6L725 View 3D Structure Click here
A0A1D6L755 View 3D Structure Click here
A0A2R8Q1T4 View 3D Structure Click here
F1Q5R8 View 3D Structure Click here
F4JLI5 View 3D Structure Click here
G3X982 View 3D Structure Click here
I1JIN7 View 3D Structure Click here
I1M510 View 3D Structure Click here
I1M7D9 View 3D Structure Click here
I6Y7N2 View 3D Structure Click here
K7KB27 View 3D Structure Click here
M1ZMM0 View 3D Structure Click here
O17892 View 3D Structure Click here
O23887 View 3D Structure Click here
O23888 View 3D Structure Click here
O54754 View 3D Structure Click here
O61198 View 3D Structure Click here
P10351 View 3D Structure Click here
P22985 View 3D Structure Click here
P47989 View 3D Structure Click here
P64557 View 3D Structure Click here
P77324 View 3D Structure Click here
Q00519 View 3D Structure Click here
Q06278 View 3D Structure Click here
Q3TYQ9 View 3D Structure Click here
Q46800 View 3D Structure Click here
Q54FB7 View 3D Structure Click here
Q5QE78 View 3D Structure Click here
Q5QE79 View 3D Structure Click here
Q5QE80 View 3D Structure Click here
Q5SGK3 View 3D Structure Click here
Q69R21 View 3D Structure Click here
Q6AUV1 View 3D Structure Click here
Q6Z351 View 3D Structure Click here