Structure of PDB 1v5e Chain A Binding Site BS01

Receptor Information

>1v5e Chain A (length=590) Species: 1377 (Aerococcus viridans)

DNKINIGLAVMKILESWGADTIYGIPSGTLSSLMDAMGEEENNVKFLQVK
HEEVGAMAAVMQSKFGGNLGVTVGSGGPGASHLINGLYDAAMDNIPVVAI
LGSRPQRELNMDAFQELNQNPMYDHIAVYNRRVAYAEQLPKLVDEAARMA
IAKRGVAVLEVPGDFAKVEIDNDQWYSSANSLRKYAPIAPAAQDIDAAVE
LLNNSKRPVIYAGIGTMGHGPAVQELARKIKAPVITTGKNFETFEWDFEA
LTGSTYRVGWKPANETILEADTVLFAGSNFPFSEVEGTFRNVDNFIQIDI
DPAMLGKRHHADVAILGDAALAIDEILNKVDAVEESAWWTANLKNIANWR
EYINMLETKEEGDLQFYQVYNAINNHADEDAIYSIDVGNSTQTSIRHLHM
TPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDV
VTNVRYNMPVINVVFSNTEYAFIKNKYEDTNKNLFGVDFTDVDYAKIAEA
QGAKGFTVSRIEDMDRVMAEAVAANKAGHTVVIDCKITQDRPIPVETLKL
DSKLYSEDEIKAYKERYEAANLVPFREYLEAEGLESKYIK

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 1v5e Chain A Residue 1601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1v5e Crystal Structure of Pyruvate oxidase containing FAD, from Aerococcus viridans
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): G215 I216 G217 T239 G240 K241 T257 Y258 R259 V260 G279 S280 N281 F282 P283 F284 D301 I302 M306 D320 A321 P412
• Binding residue (residue number reindexed from 1): G213 I214 G215 T237 G238 K239 T255 Y256 R257 V258 G277 S278 N279 F280 P281 F282 D299 I300 M304 D318 A319 P410
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): I27 S29 G30 T31 L32 E54 S77 F116 Q117 G165 R259 E286 V389 A415 M417 D442 N469 E471 Y472 F474 I475 K478 Q541
• Catalytic site (residue number reindexed from 1): I25 S27 G28 T29 L30 E52 S75 F114 Q115 G163 R257 E284 V387 A413 M415 D440 N467 E469 Y470 F472 I473 K476 Q539
• Enzyme Commision number: 1.2.3.3: pyruvate oxidase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0016491 oxidoreductase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0047112 pyruvate oxidase activity

External links

• PDB: RCSB:1v5e, PDBe:1v5e, PDBj:1v5e
• PDBsum: 1v5e
• UniProt: A9X9K8