Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help
SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

2IDK

Crystal Structure of Rat Glycine N-Methyltransferase Complexed With Folate

Functional Information from GO Data
ChainGOidnamespacecontents
A0005542molecular_functionfolic acid binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006111biological_processregulation of gluconeogenesis
A0006544biological_processglycine metabolic process
A0006546biological_processglycine catabolic process
A0006730biological_processone-carbon metabolic process
A0016594molecular_functionglycine binding
A0017174molecular_functionglycine N-methyltransferase activity
A0018013biological_processN-terminal peptidyl-glycine methylation
A0034708cellular_componentmethyltransferase complex
A0042802molecular_functionidentical protein binding
A0046500biological_processS-adenosylmethionine metabolic process
A0050843biological_processS-adenosylmethionine catabolic process
A0051289biological_processprotein homotetramerization
A0098603molecular_functionselenol Se-methyltransferase activity
A1901052biological_processobsolete sarcosine metabolic process
A1901605biological_processalpha-amino acid metabolic process
A1904047molecular_functionS-adenosyl-L-methionine binding
B0005542molecular_functionfolic acid binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006111biological_processregulation of gluconeogenesis
B0006544biological_processglycine metabolic process
B0006546biological_processglycine catabolic process
B0006730biological_processone-carbon metabolic process
B0016594molecular_functionglycine binding
B0017174molecular_functionglycine N-methyltransferase activity
B0018013biological_processN-terminal peptidyl-glycine methylation
B0034708cellular_componentmethyltransferase complex
B0042802molecular_functionidentical protein binding
B0046500biological_processS-adenosylmethionine metabolic process
B0050843biological_processS-adenosylmethionine catabolic process
B0051289biological_processprotein homotetramerization
B0098603molecular_functionselenol Se-methyltransferase activity
B1901052biological_processobsolete sarcosine metabolic process
B1901605biological_processalpha-amino acid metabolic process
B1904047molecular_functionS-adenosyl-L-methionine binding
C0005542molecular_functionfolic acid binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006111biological_processregulation of gluconeogenesis
C0006544biological_processglycine metabolic process
C0006546biological_processglycine catabolic process
C0006730biological_processone-carbon metabolic process
C0016594molecular_functionglycine binding
C0017174molecular_functionglycine N-methyltransferase activity
C0018013biological_processN-terminal peptidyl-glycine methylation
C0034708cellular_componentmethyltransferase complex
C0042802molecular_functionidentical protein binding
C0046500biological_processS-adenosylmethionine metabolic process
C0050843biological_processS-adenosylmethionine catabolic process
C0051289biological_processprotein homotetramerization
C0098603molecular_functionselenol Se-methyltransferase activity
C1901052biological_processobsolete sarcosine metabolic process
C1901605biological_processalpha-amino acid metabolic process
C1904047molecular_functionS-adenosyl-L-methionine binding
D0005542molecular_functionfolic acid binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006111biological_processregulation of gluconeogenesis
D0006544biological_processglycine metabolic process
D0006546biological_processglycine catabolic process
D0006730biological_processone-carbon metabolic process
D0016594molecular_functionglycine binding
D0017174molecular_functionglycine N-methyltransferase activity
D0018013biological_processN-terminal peptidyl-glycine methylation
D0034708cellular_componentmethyltransferase complex
D0042802molecular_functionidentical protein binding
D0046500biological_processS-adenosylmethionine metabolic process
D0050843biological_processS-adenosylmethionine catabolic process
D0051289biological_processprotein homotetramerization
D0098603molecular_functionselenol Se-methyltransferase activity
D1901052biological_processobsolete sarcosine metabolic process
D1901605biological_processalpha-amino acid metabolic process
D1904047molecular_functionS-adenosyl-L-methionine binding
Functional Information from PDB Data
site_idAC1
Number of Residues12
DetailsBINDING SITE FOR RESIDUE C2F A 1410
ChainResidue
ATYR5
DLEU207
DHIS214
DMET215
ATHR7
BLEU207
BHIS214
BMET215
BARG239
CSER3
CVAL4
CTYR5
site_idAC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE C2F B 1420
ChainResidue
ALEU207
AMET215
BSER3
BTYR5
CLEU207
CHIS214
CMET215
CARG239
DTYR5
DTHR7
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22037183","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3THR","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"3THS","evidenceCode":"ECO:0000312"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22037183","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3THS","evidenceCode":"ECO:0000312"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues20
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1NBI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"8810903","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1XVA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8810903","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1XVA","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1NBI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8810903","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XVA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues16
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues3
DetailsModified residue: {"description":"N-acetylvaline","evidences":[{"source":"PubMed","id":"2822402","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1xva
ChainResidueDetails
AGLU15
site_idCSA2
Number of Residues1
DetailsAnnotated By Reference To The Literature 1xva
ChainResidueDetails
BGLU15
site_idCSA3
Number of Residues1
DetailsAnnotated By Reference To The Literature 1xva
ChainResidueDetails
CGLU15
site_idCSA4
Number of Residues1
DetailsAnnotated By Reference To The Literature 1xva
ChainResidueDetails
DGLU15
site_idMCSA1
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
ATYR21electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
AGLY137electrostatic stabiliser, hydrogen bond acceptor
AHIS142activator
AARG175electrostatic stabiliser
ATYR194electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
site_idMCSA2
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
BTYR21electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
BGLY137electrostatic stabiliser, hydrogen bond acceptor
BHIS142activator
BARG175electrostatic stabiliser
BTYR194electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
site_idMCSA3
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
CTYR21electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
CGLY137electrostatic stabiliser, hydrogen bond acceptor
CHIS142activator
CARG175electrostatic stabiliser
CTYR194electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
site_idMCSA4
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
DTYR21electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
DGLY137electrostatic stabiliser, hydrogen bond acceptor
DHIS142activator
DARG175electrostatic stabiliser
DTYR194electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

251801

PDB entries from 2026-04-08

PDB statisticsPDBj update infoContact PDBjnumon