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1KNW

Crystal structure of diaminopimelate decarboxylase

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0005515molecular_functionprotein binding
A0008836molecular_functiondiaminopimelate decarboxylase activity
A0009085biological_processlysine biosynthetic process
A0009089biological_processlysine biosynthetic process via diaminopimelate
A0016830molecular_functioncarbon-carbon lyase activity
A0016831molecular_functioncarboxy-lyase activity
A0030170molecular_functionpyridoxal phosphate binding
A0042803molecular_functionprotein homodimerization activity
Functional Information from PDB Data
site_idAC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 A 520
ChainResidue
AMES510
AHOH704
AHOH784

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE LI A 530
ChainResidue
AHIS151
ASER152
ALYS154
AASN156
AHOH645

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE LI A 540
ChainResidue
ASER384
AARG389
APRO390
ALEU391
AHOH590
AASN303

site_idAC4
Number of Residues16
DetailsBINDING SITE FOR RESIDUE PLP A 554
ChainResidue
AALA52
ALYS54
ATHR100
AHIS191
AGLY227
AGLU268
AGLY270
AARG271
ACYS342
ATYR378
AMES510
AHOH595
AHOH602
AHOH614
AHOH629
AHOH631

site_idAC5
Number of Residues13
DetailsBINDING SITE FOR RESIDUE MES A 510
ChainResidue
ALYS54
ATHR157
AHIS191
ATYR311
AGLU343
ASER344
ATYR378
ASO4520
APLP554
AHOH609
AHOH614
AHOH704
AHOH864

Functional Information from PROSITE/UniProt
site_idPS00878
Number of Residues19
DetailsODR_DC_2_1 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. FAqKACsnihILrlMreqG
ChainResidueDetails
APHE51-GLY69

site_idPS00879
Number of Residues14
DetailsODR_DC_2_2 Orn/DAP/Arg decarboxylases family 2 signature 2. Gqd....LqAISAGGGLS
ChainResidueDetails
AGLY216-SER229

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_02120
ChainResidueDetails
ACYS342

site_idSWS_FT_FI2
Number of Residues5
DetailsBINDING: BINDING => ECO:0000305|Ref.10
ChainResidueDetails
AHIS191
AARG271
AARG307
ATYR311
AGLU343

site_idSWS_FT_FI3
Number of Residues1
DetailsBINDING: BINDING => ECO:0000269|Ref.10
ChainResidueDetails
AGLY227

site_idSWS_FT_FI4
Number of Residues1
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_02120, ECO:0000269|Ref.10
ChainResidueDetails
AGLU268

site_idSWS_FT_FI5
Number of Residues1
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_02120
ChainResidueDetails
ATYR378

site_idSWS_FT_FI6
Number of Residues1
DetailsMOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|Ref.10
ChainResidueDetails
ALYS54

Catalytic Information from CSA
site_idCSA1
Number of Residues2
DetailsAnnotated By Reference To The Literature 1bd0
ChainResidueDetails
ALYS54
ALYS163

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1bd0
ChainResidueDetails
ALYS54
AGLU268
AHIS191

224004

PDB entries from 2024-08-21

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