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1274  structures 493  species 0  interactions 11694  sequences 193  architectures

Family: Lig_chan-Glu_bd (PF10613)

Summary: Ligated ion channel L-glutamate- and glycine-binding site

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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.

Ligated ion channel L-glutamate- and glycine-binding site Provide feedback

This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, PF00060.

Literature references

  1. Ishii T, Moriyoshi K, Sugihara H, Sakurada K, Kadotani H, Yokoi M, Akazawa C, Shigemoto R, Mizuno N, Masu M, et al.; , J Biol Chem. 1993;268:2836-2843.: Molecular characterization of the family of the N-methyl-D-aspartate receptor subunits. PUBMED:8428958 EPMC:8428958

  2. Yamakura T, Shimoji K; , Prog Neurobiol. 1999;59:279-298.: Subunit- and site-specific pharmacology of the NMDA receptor channel. PUBMED:10465381 EPMC:10465381


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019594

This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine in the ionotropic glutamate receptor NMDA [ PUBMED:10465381 , PUBMED:8428958 ]. It is found in association with INTERPRO .

Ionotropic Receptors (IRs) are a variant subfamily of the Ionotropic glutamate receptors (iGluRs). In IRs, the ligand binding domain lacks one or more residues that directly contact the glutamate ligand in iGluRs [ PUBMED:20808886 ].

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 PBP (CL0177), which has the following description:

Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors [2].

The clan contains the following 27 members:

DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate Mycoplasma_p37 NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 PDT Phosphonate-bd Porphobil_deam SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_C

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
(105)
Full
(11694)
Representative proteomes UniProt
(20358)
RP15
(2234)
RP35
(4709)
RP55
(10542)
RP75
(13632)
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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
(105)
Full
(11694)
Representative proteomes UniProt
(20358)
RP15
(2234)
RP35
(4709)
RP55
(10542)
RP75
(13632)
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
(105)
Full
(11694)
Representative proteomes UniProt
(20358)
RP15
(2234)
RP35
(4709)
RP55
(10542)
RP75
(13632)
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_203 (release 22.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 105
Number in full: 11694
Average length of the domain: 112.60 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 13.18 %

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 30.0 30.0
Trusted cut-off 30.0 30.0
Noise cut-off 29.9 29.9
Model length: 116
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 Lig_chan-Glu_bd domain has been found. There are 1274 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
A0A0B4KHJ0 View 3D Structure Click here
A0A0R4ID43 View 3D Structure Click here
A0A0R4IG83 View 3D Structure Click here
A0A0R4ING5 View 3D Structure Click here
A0A1D6L242 View 3D Structure Click here
A0A1T5HUM0 View 3D Structure Click here
A0A286Y9Q6 View 3D Structure Click here
A0A286YAM5 View 3D Structure Click here
A0A286YAY2 View 3D Structure Click here
A0A2R8PY76 View 3D Structure Click here
A0A2R8Q9Y5 View 3D Structure Click here
A0A2R8QDR4 View 3D Structure Click here
A0A2R8QF68 View 3D Structure Click here
A0A2R8QFE5 View 3D Structure Click here
A0A2R8QLP2 View 3D Structure Click here
A0A3B1E9Z6 View 3D Structure Click here
A2AIR5 View 3D Structure Click here
A2BH14 View 3D Structure Click here
A2CG69 View 3D Structure Click here
B1AS29 View 3D Structure Click here
B3DGS8 View 3D Structure Click here
B8JLR6 View 3D Structure Click here
E7F101 View 3D Structure Click here
E7F1P4 View 3D Structure Click here
E7F1V8 View 3D Structure Click here
E7F3Z4 View 3D Structure Click here
E7F5R2 View 3D Structure Click here
E7F902 View 3D Structure Click here
E7FEG9 View 3D Structure Click here
E7FGL8 View 3D Structure Click here
E7FH62 View 3D Structure Click here
E9NA96 View 3D Structure Click here
E9QGN5 View 3D Structure Click here
F1QA08 View 3D Structure Click here
F1QDE5 View 3D Structure Click here
F1QS78 View 3D Structure Click here
F6P6I2 View 3D Structure Click here
G5EEH3 View 3D Structure Click here
I3NI77 View 3D Structure Click here
K7LS68 View 3D Structure Click here
O01623 View 3D Structure Click here
O15399 View 3D Structure Click here
O43424 View 3D Structure Click here
O60391 View 3D Structure Click here
P19490 View 3D Structure Click here
P19491 View 3D Structure Click here
P19492 View 3D Structure Click here
P19493 View 3D Structure Click here
P22756 View 3D Structure Click here
P23818 View 3D Structure Click here
P23819 View 3D Structure Click here
P34299 View 3D Structure Click here
P35436 View 3D Structure Click here
P35438 View 3D Structure Click here
P35439 View 3D Structure Click here
P39086 View 3D Structure Click here
P39087 View 3D Structure Click here
P42260 View 3D Structure Click here
P42261 View 3D Structure Click here
P42262 View 3D Structure Click here
P42263 View 3D Structure Click here
P42264 View 3D Structure Click here
P48058 View 3D Structure Click here
Q00959 View 3D Structure Click here
Q00960 View 3D Structure Click here
Q00961 View 3D Structure Click here
Q01097 View 3D Structure Click here
Q01098 View 3D Structure Click here
Q01812 View 3D Structure Click here
Q03391 View 3D Structure Click here
Q03445 View 3D Structure Click here
Q05586 View 3D Structure Click here
Q0E8N6 View 3D Structure Click here
Q0KI42 View 3D Structure Click here
Q0KIF2 View 3D Structure Click here
Q10914 View 3D Structure Click here
Q12879 View 3D Structure Click here
Q13002 View 3D Structure Click here
Q13003 View 3D Structure Click here
Q13224 View 3D Structure Click here
Q14957 View 3D Structure Click here
Q16099 View 3D Structure Click here
Q16478 View 3D Structure Click here
Q17697 View 3D Structure Click here
Q21415 View 3D Structure Click here
Q24418 View 3D Structure Click here
Q60934 View 3D Structure Click here
Q61625 View 3D Structure Click here
Q61626 View 3D Structure Click here
Q61627 View 3D Structure Click here
Q62640 View 3D Structure Click here
Q62645 View 3D Structure Click here
Q63226 View 3D Structure Click here
Q63273 View 3D Structure Click here
Q68Y21 View 3D Structure Click here
Q6ZM67 View 3D Structure Click here
Q8BMF5 View 3D Structure Click here
Q8MXV8 View 3D Structure Click here
Q8TCU5 View 3D Structure Click here
Q8VHN2 View 3D Structure Click here
Q91ZU9 View 3D Structure Click here
Q9R1M7 View 3D Structure Click here
Q9TVI0 View 3D Structure Click here
Q9ULK0 View 3D Structure Click here
Q9V4A0 View 3D Structure Click here
Q9VDH5 View 3D Structure Click here
Q9VIA5 View 3D Structure Click here
Q9VMP3 View 3D Structure Click here
Q9VMP4 View 3D Structure Click here
Q9VPV3 View 3D Structure Click here
Q9W365 View 3D Structure Click here
Q9W3P2 View 3D Structure Click here
Q9W581 View 3D Structure Click here
Q9Z2W8 View 3D Structure Click here
Q9Z2W9 View 3D Structure Click here
R4GDN8 View 3D Structure Click here
X1WH07 View 3D Structure Click here