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46  structures 6492  species 0  interactions 34863  sequences 277  architectures

Family: NAD_binding_10 (PF13460)

Summary: NAD(P)H-binding

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

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 annotation information from the InterPro database.

InterPro entry IPR016040

This entry represents NAD- and NADP-binding domains with a core Rossmann-type fold, which consists of 3-layers alpha/beta/alpha, where the six beta strands are parallel in the order 321456. Many different enzymes contain an NAD/NADP-binding domain, including:

  • C-terminal domain of alcohol dehydrogenases [ PUBMED:15449945 ]
  • Tyrosine-dependent oxidoreductases (also known as short-chain dehydrogenases) [ PUBMED:9174344 ]
  • N-terminal domain of glyceraldehyde-3-phosphate dehydrogenase [ PUBMED:10448043 ]
  • NAD-binding domain of formate/glycerate dehydrogenases [ PUBMED:8114093 ]
  • N-terminal domain of sirohaem synthase [ PUBMED:14595395 ]
  • N-terminal domain of lactate dehydrogenase [ PUBMED:11276087 ]
  • N-terminal domain of 6-phosphogluconate dehydrogenase (the beta-sheet is extended to 8 strands) [ PUBMED:17222187 ]
  • C-terminal domain of amino acid dehydrogenases (an extra N-terminal helix displaces the C-terminal helix [ PUBMED:8591026 ]
  • NAD-binding domain of certain potassium channels [ PUBMED:11301020 ]
  • C-terminal domain of the transcriptional repressor Rex [ PUBMED:15642260 ]
  • Ornithine cyclodeaminase [ PUBMED:15518536 ]
  • CoA-binding N-terminal domain of the alpha chain of succinyl-CoA synthetase [ PUBMED:9917402 ]

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 206 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 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 DUF2431 DUF268 DUF2855 DUF3410 DUF364 DUF43 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 K_oxygenase KR LCM Ldh_1_N LpxI_N Lycopene_cycl 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 MOLO1 Mqo MT-A70 MTS Mur_ligase N2227 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 Orbi_VP4 PALP PARP_regulatory PCMT PDH 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 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

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
(298)
Full
(34863)
Representative proteomes UniProt
(118775)
RP15
(3333)
RP35
(14275)
RP55
(32422)
RP75
(56583)
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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
(298)
Full
(34863)
Representative proteomes UniProt
(118775)
RP15
(3333)
RP35
(14275)
RP55
(32422)
RP75
(56583)
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
(298)
Full
(34863)
Representative proteomes UniProt
(118775)
RP15
(3333)
RP35
(14275)
RP55
(32422)
RP75
(56583)
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: Jackhmmer:C2D4U5
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 298
Number in full: 34863
Average length of the domain: 172.00 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 59.64 %

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 27.2 27.2
Trusted cut-off 27.2 27.2
Noise cut-off 27.1 27.1
Model length: 184
Family (HMM) version: 8
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 NAD_binding_10 domain has been found. There are 46 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
A0A0G2QC15 View 3D Structure Click here
A0A0P0VU49 View 3D Structure Click here
A0A0P0VYP9 View 3D Structure Click here
A0A0P0WH35 View 3D Structure Click here
A0A0P0WKD6 View 3D Structure Click here
A0A0R0H848 View 3D Structure Click here
A0A0R0HG02 View 3D Structure Click here
A0A0R0JI14 View 3D Structure Click here
A0A1D6GVM8 View 3D Structure Click here
A0A1D6GVM8 View 3D Structure Click here
A0A1D6I794 View 3D Structure Click here
A0A1D6I798 View 3D Structure Click here
A0A1D6K3E5 View 3D Structure Click here
A0A1D6K5G9 View 3D Structure Click here
A0A1D6KLA9 View 3D Structure Click here
A0A1D6KTY6 View 3D Structure Click here
A0A1D6L9Y9 View 3D Structure Click here
A0A1D6LHS8 View 3D Structure Click here
A0A1D6M9V8 View 3D Structure Click here
A0A1D6MQ82 View 3D Structure Click here
A0A1D6MTK5 View 3D Structure Click here
A0A1D6P4L4 View 3D Structure Click here
A0A1D6P4X3 View 3D Structure Click here
A0A1D6QB18 View 3D Structure Click here
A0A1D8PJA6 View 3D Structure Click here
A0A1D8PRL3 View 3D Structure Click here
A0A367GLB9 View 3D Structure Click here
B4FH62 View 3D Structure Click here
B4FTR5 View 3D Structure Click here
B5DF65 View 3D Structure Click here
B6SU61 View 3D Structure Click here
B6SZW0 View 3D Structure Click here
B8JMC1 View 3D Structure Click here
C0HH81 View 3D Structure Click here
C0PE12 View 3D Structure Click here
C6THR8 View 3D Structure Click here
C6TJN4 View 3D Structure Click here
F4JRN8 View 3D Structure Click here
F4JRN8 View 3D Structure Click here
F4JSP1 View 3D Structure Click here
I1J4R0 View 3D Structure Click here
I1JMB3 View 3D Structure Click here
I1JU43 View 3D Structure Click here
I1K333 View 3D Structure Click here
I1KG15 View 3D Structure Click here
I1KG15 View 3D Structure Click here
I1KH83 View 3D Structure Click here
I1KSG4 View 3D Structure Click here
I1KSG4 View 3D Structure Click here
I1KVW6 View 3D Structure Click here
I1KVW6 View 3D Structure Click here
I1KX15 View 3D Structure Click here
I1L506 View 3D Structure Click here
I1LJY2 View 3D Structure Click here
I1LQ66 View 3D Structure Click here
I1LQL6 View 3D Structure Click here
I1M1C4 View 3D Structure Click here
I1MF65 View 3D Structure Click here
I1MJX7 View 3D Structure Click here
I1N2I4 View 3D Structure Click here
J9SKH3 View 3D Structure Click here
K7KQJ6 View 3D Structure Click here
K7KQJ6 View 3D Structure Click here
K7MFW6 View 3D Structure Click here
K7U6M0 View 3D Structure Click here
K7U6M0 View 3D Structure Click here
O80934 View 3D Structure Click here
O82219 View 3D Structure Click here
P30043 View 3D Structure Click here
P45469 View 3D Structure Click here
P75822 View 3D Structure Click here
Q04304 View 3D Structure Click here
Q10A77 View 3D Structure Click here
Q10LH0 View 3D Structure Click here
Q1H537 View 3D Structure Click here
Q2FV44 View 3D Structure Click here
Q2FWB1 View 3D Structure Click here
Q2G0Y0 View 3D Structure Click here
Q336P0 View 3D Structure Click here
Q54LW0 View 3D Structure Click here
Q54S81 View 3D Structure Click here
Q54U38 View 3D Structure Click here
Q54WF5 View 3D Structure Click here
Q5DX36 View 3D Structure Click here
Q5Z8V8 View 3D Structure Click here
Q5Z8V8 View 3D Structure Click here
Q69SX2 View 3D Structure Click here
Q6EUK5 View 3D Structure Click here
Q6EUK5 View 3D Structure Click here
Q6NMC1 View 3D Structure Click here
Q6YXY0 View 3D Structure Click here
Q6YXY0 View 3D Structure Click here
Q6ZI86 View 3D Structure Click here
Q7XVF8 View 3D Structure Click here
Q852A3 View 3D Structure Click here
Q8H0U5 View 3D Structure Click here
Q8H124 View 3D Structure Click here
Q8W4D6 View 3D Structure Click here
Q8W4D6 View 3D Structure Click here
Q90Z77 View 3D Structure Click here
Q923D2 View 3D Structure Click here
Q93VH5 View 3D Structure Click here
Q949S7 View 3D Structure Click here
Q94EG6 View 3D Structure Click here
Q9BUP3 View 3D Structure Click here
Q9FVR6 View 3D Structure Click here
Q9M0B3 View 3D Structure Click here
Q9SK66 View 3D Structure Click here
Q9STF2 View 3D Structure Click here
Q9VH72 View 3D Structure Click here
Q9Y7K0 View 3D Structure Click here
Q9Z2G9 View 3D Structure Click here