Structure of PDB 2bc1 Chain A Binding Site BS01

Receptor Information
>2bc1 Chain A (length=473) Species: 1314 (Streptococcus pyogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQQMGRTLYDDDDKDRWGSKIVVVGANHAGTACIKTMLTNYGDANEIVVF
DQNSNISFLGSGMALWIGEQIAGPEGLFYSDKEELESLGAKVYMESPVQS
IDYDAKTVTALVDGKNHVETYDKLIFATGSQPILPPIKGAEIKEGSLEFE
ATLENLQFVKLYQNSADVIAKLENKDIKRVAVVGAGYIGVELAEAFQRKG
KEVVLIDVVDTCLAGYYDRDLTDLMAKNMEEHGIQLAFGETVKEVAGNGK
VEKIITDKNEYDVDMVILAVGFRPNTTLGNGKIDLFRNGAFLVNKRQETS
IPGVYAIGDCATIYDNATRDTNYIALASNAVRTGIVAAHNACGTDLEGIG
VQGSNGISIYGLHMVSTGLTLEKAKRLGFDAAVTEYTDNQKPEFIEHGNF
PVTIKIVYDKDSRRILGAQMAAREDVSMGIHMFSLAIQEGVTIEKLALTD
IFFLPHFNKPYNYITMAALGAKD
Ligand information
Ligand IDFAD
InChIInChI=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
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=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 1.5.0Cc1cc2c(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 1.5.0Cc1cc2c(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 3.341Cc1cc2N=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 10.04O=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
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain2bc1 Chain A Residue 457 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2bc1 Structural Analysis of Streptococcus pyogenes NADH Oxidase: Conformational Dynamics Involved in Formation of the C(4a)-Peroxyflavin Intermediate.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		V7 G8 N10 H11 A12 F33 D34 Q35 G43 S44 M46 V81 A110 T111 G112 K143 Y170 I171 G291 D292 A308 L309 A310
Binding residue
(residue number reindexed from 1)		V24 G25 N27 H28 A29 F50 D51 Q52 G60 S61 M63 V98 A127 T128 G129 K160 Y187 I188 G308 D309 A325 L326 A327
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H11 I39 G43 S44 V314
Catalytic site (residue number reindexed from 1) H28 I56 G60 S61 V331
Enzyme Commision number 1.6.3.4: NADH oxidase (H2O-forming).
Gene Ontology
Molecular Function
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0016491 oxidoreductase activity
Biological Process
GO:1902600 proton transmembrane transport

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2bc1, PDBe:2bc1, PDBj:2bc1
PDBsum2bc1
PubMed26506002
UniProtQ5XC60|NAOX_STRP6 NADH oxidase (Gene Name=M6_Spy0868)

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