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343  structures 6958  species 0  interactions 77886  sequences 712  architectures

Family: FAD_binding_3 (PF01494)

Summary: FAD binding domain

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 "Monooxygenase". More...

Monooxygenase Edit Wikipedia article

Structure of the TetX monooxygenase in complex with the substrate 7-Iodtetracycline.[1]
Symbol FAD_binding_3
Pfam PF01494
InterPro IPR002938
SCOP 2phh

Monooxygenases are enzymes that incorporate one hydroxyl group into substrates in many metabolic pathways. In this reaction, the two atoms of dioxygen are reduced to one hydroxyl group and one H2O molecule by the concomitant oxidation of NAD(P)H.[2][3] One important subset of the monooxygenases, the cytochrome P450 omega hydroxylases, is used by cells to metabolize arachidonic acid (i.e. eicosatetraenoic acid) to the cell signaling molecules, 20-hydroxyeicosatetraenoic acid or to reduce or totally inactivate the activate signaling molecules for example by hydroxylating leukotriene B4 to 20-hydroxy-leukotriene B5, 5-hydroxyeicosatetraenoic acid to 5,20-dihydroxyeicosatetraenoic acid, 5-oxo-eicosatetraenoic acid to 5-oxo-20-hydroxyeicosatetraenoic acid, 12-hydroxyeicosatetraenoic acid to 12,20-dihydroxyeicosatetraenoic acid, and epoxyeicosatrienoic acids to 20-hydroxy-epoxyeicosatrienoic acids.


They are classified as oxidoreductase enzymes that catalyzes an electron transfer.

Related structures


Human proteins containing this domain


See also


  1. ^ PDB: 2Y6Q​; Volkers G, Palm GJ, Weiss MS, Wright GD, Hinrichs W (April 2011). "Structural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase". FEBS Lett. 585 (7): 1061–6. doi:10.1016/j.febslet.2011.03.012. PMID 21402075. 
  2. ^ Harayama S, Kok M, Neidle EL (1992). "Functional and evolutionary relationships among diverse oxygenases". Annu. Rev. Microbiol. 46: 565–601. doi:10.1146/annurev.mi.46.100192.003025. PMID 1444267. 
  3. ^ Schreuder HA, van Berkel WJ, Eppink MH, Bunthol C (1999). "Phe161 and Arg166 variants of p-hydroxybenzoate hydroxylase. Implications for NADPH recognition and structural stability". FEBS Lett. 443 (3): 251–255. doi:10.1016/S0014-5793(98)01726-8. PMID 10025942. 

External links

This article incorporates text from the public domain Pfam and InterPro IPR002938

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.

FAD binding domain Provide feedback

This domain is involved in FAD binding in a number of enzymes.

Literature references

  1. Schreuder HA, van der Laan JM, Swarte MB, Kalk KH, Hol WG, Drenth J; , Proteins 1992;14:178-190.: Crystal structure of the reduced form of p-hydroxybenzoate hydroxylase refined at 2.3A resolution. PUBMED:1409567 EPMC:1409567

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002938

This domain is involved in FAD binding in a number of enzymes.

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 NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 209 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 BMT5-like BpsA_C CARME CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF268 DUF2855 DUF3410 DUF364 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C KR LCM Ldh_1_N LpxI_N Lycopene_cycl Lys_Orn_oxgnase Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MmeI_Mtase MOLO1 Mqo MT-A70 MTS Mur_ligase N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall OpcA_G6PD_assem Orbi_VP4 PALP PARP_regulatory PCMT PDH_N PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth SRR1 TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N


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...

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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.

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Representative proteomes UniProt

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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.

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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...


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_549 (release 4.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 19
Number in full: 77886
Average length of the domain: 276.80 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 60.65 %

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 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 349
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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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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_3 domain has been found. There are 343 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
A0A0P0VBL5 View 3D Structure Click here
A0A0P0VKJ1 View 3D Structure Click here
A0A0P0VT64 View 3D Structure Click here
A0A0P0VT70 View 3D Structure Click here
A0A0P0VT72 View 3D Structure Click here
A0A0P0WAA7 View 3D Structure Click here
A0A0P0WM81 View 3D Structure Click here
A0A0P0X6B3 View 3D Structure Click here
A0A0R0EU03 View 3D Structure Click here
A0A0R0I082 View 3D Structure Click here
A0A0R0K3Y5 View 3D Structure Click here
A0A0R0KJT4 View 3D Structure Click here
A0A1D6E9L1 View 3D Structure Click here
A0A1D6GDN4 View 3D Structure Click here
A0A1D6HAR5 View 3D Structure Click here
A0A1D6HAR6 View 3D Structure Click here
A0A1D6IBV2 View 3D Structure Click here
A0A1D6J6Y1 View 3D Structure Click here
A0A1D6J7P5 View 3D Structure Click here
A0A1D6K0M0 View 3D Structure Click here
A0A1D6M4A4 View 3D Structure Click here
A0A1D6MQC2 View 3D Structure Click here
A0A1D6PK39 View 3D Structure Click here
A0A1D8PTL1 View 3D Structure Click here
A0A2R8RWQ2 View 3D Structure Click here
A1Z746 View 3D Structure Click here
A4HT15 View 3D Structure Click here
A4I2I2 View 3D Structure Click here
B4FME7 View 3D Structure Click here
B5BM30 View 3D Structure Click here
B6TDR5 View 3D Structure Click here
B7ZXZ6 View 3D Structure Click here
D3ZBP4 View 3D Structure Click here
D3ZGN7 View 3D Structure Click here
D4A1F2 View 3D Structure Click here
E7F9T0 View 3D Structure Click here
F1QH17 View 3D Structure Click here
F1QWK4 View 3D Structure Click here
F1RA39 View 3D Structure Click here
F1RAX8 View 3D Structure Click here