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4Q3B

PylD cocrystallized with L-Lysine-Ne-D-lysine and NAD+

Functional Information from GO Data
ChainGOidnamespacecontents
A0008652biological_processamino acid biosynthetic process
A0016491molecular_functionoxidoreductase activity
B0008652biological_processamino acid biosynthetic process
B0016491molecular_functionoxidoreductase activity
C0008652biological_processamino acid biosynthetic process
C0016491molecular_functionoxidoreductase activity
D0008652biological_processamino acid biosynthetic process
D0016491molecular_functionoxidoreductase activity
Functional Information from PDB Data
site_idAC1
Number of Residues24
DetailsBINDING SITE FOR RESIDUE NAI A 901
ChainResidue
AALA2
APRO205
ACYS206
ATHR209
APRO224
AILE226
AGLU245
APRO246
ALEU247
AMG903
A2YF904
AASN121
AHOH1002
AHOH1004
AHOH1040
AHOH1101
AHOH1120
AGLY150
ALYS151
AVAL152
AASP171
AALA172
AALA203
ATHR204

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA A 902
ChainResidue
AGLU202
ATHR204
ACYS206
APRO227
AHOH1061

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 903
ChainResidue
ATYR129
AGLU245
ALEU247
AILE249
AGLY250
ANAI901

site_idAC4
Number of Residues17
DetailsBINDING SITE FOR RESIDUE 2YF A 904
ChainResidue
ALEU3
ALEU4
AVAL53
AGLY58
AILE59
AILE60
APHE63
AALA103
AASP104
AASN121
APRO246
ANAI901
AHOH1010
AHOH1024
AHOH1031
AHOH1051
AHOH1101

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 905
ChainResidue
ASER134
ATYR136
AALA139
ASER141

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 906
ChainResidue
ASER45
AGLN72
AGLY75
APHE76
AASP164
AHOH1052

site_idAC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE GOL A 907
ChainResidue
ATHR5
AASP7

site_idAC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 908
ChainResidue
ALYS18
AALA19
AALA22
ALEU242
AALA244
AHOH1111
AHOH1116

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 909
ChainResidue
ALEU38
ATYR39
AHOH1062
AHOH1112
AHOH1118
BARG135

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL A 910
ChainResidue
APHE165
AARG166
AVAL167
AGLY185
AILE187

site_idBC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE GOL A 911
ChainResidue
APHE154
AHOH1044

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 912
ChainResidue
AGLU131
ASER134
ALYS163
APHE165
AHOH1089
AHOH1128

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL A 913
ChainResidue
ASER21
AHOH1077
BLYS47
BPHE79
BEDO906

site_idBC5
Number of Residues28
DetailsBINDING SITE FOR RESIDUE NAI B 901
ChainResidue
BLYS151
BVAL152
BTYR170
BASP171
BALA172
BASP173
BALA203
BTHR204
BPRO205
BTHR209
BPRO224
BILE226
BGLU245
BPRO246
BLEU247
BMG903
B2YF904
BHOH1002
BHOH1050
BHOH1060
BHOH1113
BHOH1119
BHOH1129
BHOH1130
BALA2
BASN121
BTHR125
BGLY150

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 902
ChainResidue
BGLU202
BTHR204
BCYS206
BPRO227
BHOH1009

site_idBC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG B 903
ChainResidue
BTYR129
BGLU245
BLEU247
BILE249
BGLY250
BNAI901

site_idBC8
Number of Residues16
DetailsBINDING SITE FOR RESIDUE 2YF B 904
ChainResidue
BLEU3
BLEU4
BVAL53
BGLY58
BILE59
BILE60
BPHE63
BALA103
BASN121
BPRO246
BNAI901
BHOH1006
BHOH1010
BHOH1034
BHOH1052
BHOH1113

site_idBC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 905
ChainResidue
BLYS32
BLYS36
BSER43
BHOH1061

site_idCC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 906
ChainResidue
AGLN17
AGOL913
AHOH1078
BASP82
BGLU91
BASN95

site_idCC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 907
ChainResidue
AALA192
BLYS196
BGLU217

site_idCC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL B 908
ChainResidue
BTHR41
BPHE42
BLEU259
BHOH1029
BHOH1036

site_idCC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL B 909
ChainResidue
AGLU158
AVAL161
AGLN162
AASN183
ALEU184
BLYS36
BTHR41
BPHE42

site_idCC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL B 910
ChainResidue
BLEU9
BILE10
BASN11
BILE12
BASN62
BALA65
BSER66
BPEG916
BHOH1057

site_idCC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL B 911
ChainResidue
ALYS32
ATYR73
AHOH1012
BGLN72
BASP77
BSER78
BHOH1117
BHOH1125

site_idCC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE GOL B 912
ChainResidue
BLEU38

site_idCC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL B 913
ChainResidue
BALA19
BARG235
BLEU242
BALA244

site_idCC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PEG B 914
ChainResidue
AALA37
AARG135
ALYS163
BGLN24
BGLU25
BGLY28
BHOH1088

site_idDC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PEG B 915
ChainResidue
AVAL53
AASP85
AMET102
BASP85
BMET102

site_idDC2
Number of Residues13
DetailsBINDING SITE FOR RESIDUE PEG B 916
ChainResidue
ALEU9
AASN11
AILE12
AASN62
AALA65
ASER66
AALA69
AHOH1086
BASN13
BGOL910
BHOH1019
BHOH1056
BHOH1059

site_idDC3
Number of Residues24
DetailsBINDING SITE FOR RESIDUE NAI C 901
ChainResidue
BALA207
CALA2
CASN121
CTHR125
CGLY150
CLYS151
CVAL152
CASP171
CALA172
CASP173
CLEU176
CALA203
CTHR204
CPRO205
CPRO224
CILE226
CGLU245
CPRO246
CLEU247
CMG903
C2YF904
CEDO905
CHOH1008
CHOH1018

site_idDC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA C 902
ChainResidue
CGLU202
CTHR204
CCYS206
CPRO227
CALA229
CHOH1017

site_idDC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG C 903
ChainResidue
CTYR129
CGLU245
CLEU247
CILE249
CGLY250
CNAI901

site_idDC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE 2YF C 904
ChainResidue
CLEU3
CLEU4
CPRO52
CVAL53
CGLY58
CILE59
CILE60
CPHE63
CALA103
CLEU247
CNAI901
CEDO905
CHOH1007
CHOH1009
CHOH1012

site_idDC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 905
ChainResidue
CASP105
CGLN122
CNAI901
C2YF904

site_idDC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO C 906
ChainResidue
DLYS36

site_idDC9
Number of Residues27
DetailsBINDING SITE FOR RESIDUE NAI D 901
ChainResidue
DALA2
DASN121
DTHR125
DVAL147
DGLY150
DLYS151
DVAL152
DTYR170
DASP171
DALA172
DLEU176
DALA203
DTHR204
DPRO205
DCYS206
DTHR209
DPRO224
DILE226
DGLU245
DPRO246
DLEU247
DMG903
D2YF904
DHOH1004
DHOH1016
DHOH1017
DHOH1025

site_idEC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA D 902
ChainResidue
DGLU202
DTHR204
DCYS206
DPRO227
DALA229
DHOH1008

site_idEC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG D 903
ChainResidue
DTYR129
DGLU245
DLEU247
DILE249
DGLY250
DNAI901

site_idEC3
Number of Residues15
DetailsBINDING SITE FOR RESIDUE 2YF D 904
ChainResidue
DLEU3
DLEU4
DPRO52
DVAL53
DGLY58
DILE59
DILE60
DPHE63
DALA103
DASN121
DNAI901
DHOH1001
DHOH1005
DHOH1020
DHOH1022

site_idEC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL D 905
ChainResidue
DASP85
DTYR89
DMET102

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:24916332, ECO:0007744|PDB:4Q39
ChainResidueDetails
ALEU4
CVAL53
CILE60
CALA103
DLEU4
DVAL53
DILE60
DALA103
AVAL53
AILE60
AALA103
BLEU4
BVAL53
BILE60
BALA103
CLEU4

site_idSWS_FT_FI2
Number of Residues28
DetailsBINDING: BINDING => ECO:0000269|PubMed:23720358, ECO:0000269|PubMed:24916332, ECO:0007744|PDB:4JK3, ECO:0007744|PDB:4Q3D
ChainResidueDetails
ALYS151
BASP171
BCYS206
BPRO224
BILE226
BGLU245
CLYS151
CVAL152
CASP171
CCYS206
CPRO224
AVAL152
CILE226
CGLU245
DLYS151
DVAL152
DASP171
DCYS206
DPRO224
DILE226
DGLU245
AASP171
ACYS206
APRO224
AILE226
AGLU245
BLYS151
BVAL152

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PDB entries from 2024-08-07

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