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2QGH

Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori complexed with L-lysine

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0008652biological_processamino acid biosynthetic process
A0008836molecular_functiondiaminopimelate decarboxylase activity
A0009085biological_processlysine biosynthetic process
A0009089biological_processlysine biosynthetic process via diaminopimelate
A0016829molecular_functionlyase activity
A0016830molecular_functioncarbon-carbon lyase activity
A0016831molecular_functioncarboxy-lyase activity
A0030170molecular_functionpyridoxal phosphate binding
Functional Information from PDB Data
site_idAC1
Number of Residues15
DetailsBINDING SITE FOR RESIDUE PLP A 406
ChainResidue
AALA44
AARG262
ATYR358
ALYS407
AHOH1004
AHOH1011
AHOH1015
AASP65
AHIS185
ASER188
AGLY224
AGLY225
AGLU259
APRO260
AGLY261

site_idAC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE LYS A 407
ChainResidue
AILE148
AARG262
AARG298
ATYR302
ACYS329
AGLU330
ATYR358
AMET362
ATYR366

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 1003
ChainResidue
ALEU101
AASN104
AILE105
ALEU108
AALA130
AARG131

Functional Information from PROSITE/UniProt
site_idPS00878
Number of Residues19
DetailsODR_DC_2_1 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. YAlKANsnlsILslLahlE
ChainResidueDetails
ATYR43-GLU61

site_idPS00879
Number of Residues16
DetailsODR_DC_2_2 Orn/DAP/Arg decarboxylases family 2 signature 2. Algid..LrFFDVGGGIG
ChainResidueDetails
AALA212-GLY227

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_02120
ChainResidueDetails
ACYS329

site_idSWS_FT_FI2
Number of Residues1
DetailsBINDING: BINDING => ECO:0000269|PubMed:18508763
ChainResidueDetails
AGLY225

site_idSWS_FT_FI3
Number of Residues1
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_02120, ECO:0000269|PubMed:18508763
ChainResidueDetails
AGLU259

site_idSWS_FT_FI4
Number of Residues5
DetailsBINDING: BINDING => ECO:0000305|PubMed:18508763
ChainResidueDetails
AARG262
AARG298
ATYR302
AGLU330
ATYR358

site_idSWS_FT_FI5
Number of Residues1
DetailsMOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:18508763
ChainResidueDetails
ALYS46

218853

PDB entries from 2024-04-24

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