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1MLZ

Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the trans-isomer of amiclenomycin.

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0004015molecular_functionadenosylmethionine-8-amino-7-oxononanoate transaminase activity
A0005737cellular_componentcytoplasm
A0008483molecular_functiontransaminase activity
A0009102biological_processbiotin biosynthetic process
A0030170molecular_functionpyridoxal phosphate binding
A0042803molecular_functionprotein homodimerization activity
B0003824molecular_functioncatalytic activity
B0004015molecular_functionadenosylmethionine-8-amino-7-oxononanoate transaminase activity
B0005737cellular_componentcytoplasm
B0008483molecular_functiontransaminase activity
B0009102biological_processbiotin biosynthetic process
B0030170molecular_functionpyridoxal phosphate binding
B0042803molecular_functionprotein homodimerization activity
Functional Information from PDB Data
site_idAC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE TZA A 431
ChainResidue
ATRP52
ATYR144
ALYS274
AARG391
APHE393
APLP430
AHOH432
AHOH439

site_idAC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE TZA B 531
ChainResidue
BTRP53
BTYR144
BARG391
BPHE393
BPLP530
BHOH4034
BHOH4035
BHOH4081
BTRP52

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE NA A 501
ChainResidue
AVAL96
ATHR99
APRO100
ALEU103

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 502
ChainResidue
BVAL96
BTHR99
BPRO100
BLEU103
BHOH2057

site_idAC5
Number of Residues13
DetailsBINDING SITE FOR RESIDUE PLP A 430
ChainResidue
AGLY112
ASER113
ATYR144
AHIS145
AASP245
AILE247
ALYS274
ATZA431
AHOH435
AHOH443
AHOH4111
BPRO308
BTHR309

site_idAC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE PLP B 530
ChainResidue
APRO308
ATHR309
AHOH2004
BTRP53
BGLY112
BSER113
BHIS145
BGLU211
BASP245
BILE247
BLYS274
BTZA531
BHOH2002
BHOH4017
BHOH4128

Functional Information from PROSITE/UniProt
site_idPS00600
Number of Residues38
DetailsAA_TRANSFER_CLASS_3 Aminotransferases class-III pyridoxal-phosphate attachment site. LIaDEIat.GFgRtGklfacehaeiap....DILclGKaltGG
ChainResidueDetails
ALEU242-GLY279

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12218056, ECO:0007744|PDB:1MLY, ECO:0007744|PDB:1QJ3
ChainResidueDetails
ATRP52
ALYS274
BTRP52
BLYS274

site_idSWS_FT_FI2
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1DTY, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S07
ChainResidueDetails
AGLY112
APRO308
BGLY112
BPRO308

site_idSWS_FT_FI3
Number of Residues2
DetailsBINDING: BINDING => ECO:0000305|PubMed:10452893
ChainResidueDetails
ATYR144
BTYR144

site_idSWS_FT_FI4
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S07
ChainResidueDetails
AASP245
BASP245

site_idSWS_FT_FI5
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0007744|PDB:1QJ3
ChainResidueDetails
AGLY307
BGLY307

site_idSWS_FT_FI6
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12218056, ECO:0007744|PDB:1MLY, ECO:0007744|PDB:1MLZ, ECO:0007744|PDB:1QJ3
ChainResidueDetails
AARG391
BARG391

site_idSWS_FT_FI7
Number of Residues2
DetailsSITE: Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM => ECO:0000305
ChainResidueDetails
ATYR17
BTYR17

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1DTY, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S06, ECO:0007744|PDB:1S08, ECO:0007744|PDB:1S09, ECO:0007744|PDB:1S0A
ChainResidueDetails
ALYS274
BLYS274

Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1b8g
ChainResidueDetails
AASP245
ATYR144
BILE83

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1b8g
ChainResidueDetails
AILE83
BASP245
BTYR144

site_idCSA3
Number of Residues3
DetailsAnnotated By Reference To The Literature 1b8g
ChainResidueDetails
AASP245
ALYS274
ATYR144

site_idCSA4
Number of Residues3
DetailsAnnotated By Reference To The Literature 1b8g
ChainResidueDetails
BASP245
BLYS274
BTYR144

site_idCSA5
Number of Residues3
DetailsAnnotated By Reference To The Literature 1b8g
ChainResidueDetails
AASP245
ALYS274
ATYR168

site_idCSA6
Number of Residues3
DetailsAnnotated By Reference To The Literature 1b8g
ChainResidueDetails
BASP245
BLYS274
BTYR168

site_idMCSA1
Number of Residues4
DetailsM-CSA 249
ChainResidueDetails
ATYR17electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
ATYR144hydrogen bond acceptor, steric role, van der waals interaction
AASP245electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
ALYS274covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_idMCSA2
Number of Residues4
DetailsM-CSA 249
ChainResidueDetails
BTYR17electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
BTYR144hydrogen bond acceptor, steric role, van der waals interaction
BASP245electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
BLYS274covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

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PDB entries from 2024-07-31

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