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1DGD

AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE

Functional Information from GO Data
ChainGOidnamespacecontents
A0008453molecular_functionalanine-glyoxylate transaminase activity
A0008483molecular_functiontransaminase activity
A0009436biological_processglyoxylate catabolic process
A0016829molecular_functionlyase activity
A0016831molecular_functioncarboxy-lyase activity
A0019481biological_processL-alanine catabolic process, by transamination
A0030170molecular_functionpyridoxal phosphate binding
A0047432molecular_function2,2-dialkylglycine decarboxylase (pyruvate) activity
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA A 435
ChainResidue
AALA95
ATHR98
APRO99
ALEU102
AHOH540

site_idAC2
Number of Residues16
DetailsBINDING SITE FOR RESIDUE PLP A 437
ChainResidue
ATHR110
AGLY111
AALA112
AASN115
ATRP138
AHIS139
AGLU210
AASP243
AALA245
AGLN246
ALYS272
ATHR302
ATHR303
AMES434
AHOH555
AHOH557

site_idAC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE MES A 434
ChainResidue
AGLN52
ATRP138
AALA152
ASER215
AGLN246
ALYS272
AARG406
APLP437

site_idACT
Number of Residues22
DetailsACTIVE SITE: THE COFACTOR PLP IS COVALENTLY BOUND
ChainResidue
AGLN52
AGLU210
ASER214
ASER215
AASP243
AALA245
AGLN246
ALYS272
APLP437
ATYR301
ATHR303
AMET53
AASN394
AARG406
AMES434
APHE79
ATHR110
AGLY111
AASN115
ASER137
ATRP138
AMET141

site_idME1
Number of Residues5
DetailsMETAL BINDING SITE 1 (NEAR THE ACTIVE SITE): LIGANDS TO THE LI+ ION ARE INDICATED
ChainResidue
ALEU78
AASP307
AHOH539
AHOH552
ALI436

site_idME2
Number of Residues6
DetailsMETAL BINDING SITE 2: LIGANDS TO THE NA+ ION ARE INDICATED
ChainResidue
AALA95
ATHR98
APRO99
ALEU102
AHOH540
ANA435

Functional Information from PROSITE/UniProt
site_idPS00600
Number of Residues38
DetailsAA_TRANSFER_CLASS_3 Aminotransferases class-III pyridoxal-phosphate attachment site. LIlDEAqt.GVgRtGtmfacqrdgvtp....DILtlSKtlgAG
ChainResidueDetails
ALEU240-GLY277

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsMOD_RES: N6-(pyridoxal phosphate)lysine
ChainResidueDetails
ATHR273

Catalytic Information from CSA
site_idMCSA1
Number of Residues6
DetailsM-CSA 482
ChainResidueDetails
AHIS139steric role
APRO211steric role, transition state stabiliser
AGLU244electrostatic stabiliser, increase electrophilicity
ATHR247electrostatic stabiliser
ATHR273covalent catalysis, proton shuttle (general acid/base)
AILE407steric role, transition state stabiliser

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PDB entries from 2024-04-17

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