Structure of PDB 6qii Chain B Binding Site BS03

Receptor Information
>6qii Chain B (length=291) Species: 1434108 (Methanosarcina barkeri MS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEDPYLGKYVTCVSARSTDKEILKKAQDGGIATALMVYALEEGFIDGTI
VAGEGDKPWQPKPVVAMTREDILKARGTRYNISPQISWLKEATRSFGLDK
VGVTGVCCQMQAVRKAQLYPINMRDVPGKVAFTVGLFCMENFSYKSLQSI
VEDHANQSLGSVKKMEITKGKFWVYTERGNVATVPLKATHKYEQPGCHVC
LDYVSNLADISTGSVGSPDGWSTVFIRTKVGNEIWSKAVADGMFETKPIE
EVKPGLDLLRKLAKEKIDKNQKTVEERKTFGINKGLRNPYA
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 chain6qii Chain B Residue 302 [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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PDB6qii X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		A27 Q28 D29 G31 I32 A33 T34 A52 A75 G77 T78 R79 Y80 L136 F137 C138 M139 N141 Y203 G213 S214 V215
Binding residue
(residue number reindexed from 1)		A27 Q28 D29 G31 I32 A33 T34 A52 A75 G77 T78 R79 Y80 L136 F137 C138 M139 N141 Y203 G213 S214 V215
Annotation score1
Enzymatic activity
Enzyme Commision number 1.12.98.1: coenzyme F420 hydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016151 nickel cation binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050454 coenzyme F420 hydrogenase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0052592 oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor

View graph for
Molecular Function
External links
PDB RCSB:6qii, PDBe:6qii, PDBj:6qii
PDBsum6qii
PubMed31591784
UniProtA0A0E3QWH3

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