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1X7D

Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0008473molecular_functionornithine cyclodeaminase activity
A0008652biological_processamino acid biosynthetic process
A0016829molecular_functionlyase activity
A0055129biological_processL-proline biosynthetic process
B0000166molecular_functionnucleotide binding
B0008473molecular_functionornithine cyclodeaminase activity
B0008652biological_processamino acid biosynthetic process
B0016829molecular_functionlyase activity
B0055129biological_processL-proline biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA A 1501
ChainResidue
AALA224
AVAL225
AGLY227
ASER293
AHOH1513
AHOH1879

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA B 1502
ChainResidue
BSER293
BHOH3176
BHOH3315
BALA224
BVAL225
BGLY227

site_idAC3
Number of Residues31
DetailsBINDING SITE FOR RESIDUE NAD B 1301
ChainResidue
ALYS331
AORN1102
AHOH1516
AHOH1668
BTHR84
BARG112
BTHR113
BGLY138
BALA139
BGLN140
BASP161
BTHR162
BVAL201
BTHR202
BALA203
BILE210
BVAL225
BGLY226
BASP228
BLYS232
BSER293
BVAL294
BGLY295
BHOH3165
BHOH3166
BHOH3170
BHOH3209
BHOH3223
BHOH3323
BHOH3387
BHOH3538

site_idAC4
Number of Residues31
DetailsBINDING SITE FOR RESIDUE NAD A 1302
ChainResidue
ATHR84
AARG112
ATHR113
AGLY138
AALA139
AGLN140
AASP161
ATHR162
AVAL201
ATHR202
AALA203
AILE210
AVAL225
AGLY226
AASP228
ALYS232
ASER293
AVAL294
AGLY295
AORN1101
AHOH1503
AHOH1504
AHOH1512
AHOH1519
AHOH1559
AHOH1598
AHOH1610
AHOH1686
AHOH1695
AHOH1801
BLYS331

site_idAC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE ORN A 1101
ChainResidue
AARG45
AVAL54
AGLU56
ALYS69
AVAL71
AASN72
AGLY73
AVAL85
AARG112
AASP228
AVAL294
AGLY295
ANAD1302
AHOH1558
AHOH1642
AHOH1695

site_idAC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ORN A 1102
ChainResidue
BARG112
BASP228
BVAL294
BGLY295
BNAD1301
BHOH3207
AHOH1611
BARG45
BVAL54
BGLU56
BMSE58
BLYS69
BASN72
BGLY73
BVAL85

site_idAC7
Number of Residues9
DetailsBINDING SITE FOR RESIDUE MES B 3158
ChainResidue
AGLN283
ASER284
AGLN287
AARG338
AHOH1793
BHIS15
BGLU176
BTYR177
BHOH3259

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MPD A 1401
ChainResidue
AGLN38
AALA39
APHE40
AASP62
ALYS63
AMPD1402

site_idAC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MPD A 1402
ChainResidue
AGLN38
AALA39
AMPD1401
BLEU216
BASN242
BSER286
BHOH3440

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MPD A 1403
ChainResidue
ASER64
AARG65
ALEU91
AASP93
AVAL100
AHOH1592

site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MPD A 1404
ChainResidue
ATYR3
AALA311
AGLU312
AMSE316

site_idBC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MPD B 1405
ChainResidue
BTYR3
BALA311
BGLU312
BGLY315
BMSE316

site_idBC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE MPD B 1406
ChainResidue
BSER64
BARG65
BALA92
BASP93
BVAL100
BLEU308
BHOH3267
BHOH3513

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Proton donor/acceptor => ECO:0000305|PubMed:15518536, ECO:0007744|PDB:1X7D
ChainResidueDetails
AASP228
BASP228

site_idSWS_FT_FI2
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:15518536, ECO:0007744|PDB:1X7D
ChainResidueDetails
AARG45
ALYS69
AASP228
AVAL294
BARG45
BLYS69
BASP228
BVAL294

site_idSWS_FT_FI3
Number of Residues18
DetailsBINDING: BINDING => ECO:0000269|PubMed:15518536, ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D
ChainResidueDetails
ATHR84
BTHR84
BARG112
BALA139
BASP161
BTHR202
BVAL225
BLYS232
BSER293
BLYS331
AARG112
AALA139
AASP161
ATHR202
AVAL225
ALYS232
ASER293
ALYS331

Catalytic Information from CSA
site_idCSA1
Number of Residues2
Detailsa catalytic site defined by CSA, PubMed 15518536
ChainResidueDetails
AASP228
AGLU56

site_idCSA2
Number of Residues2
Detailsa catalytic site defined by CSA, PubMed 15518536
ChainResidueDetails
BASP228
BGLU56

site_idMCSA1
Number of Residues2
DetailsM-CSA 717
ChainResidueDetails
AVAL60increase nucleophilicity, proton acceptor, proton donor
AGLU256proton acceptor, proton donor

site_idMCSA2
Number of Residues2
DetailsM-CSA 717
ChainResidueDetails
BVAL60increase nucleophilicity, proton acceptor, proton donor
BGLU256proton acceptor, proton donor

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PDB entries from 2025-06-18

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