Structure of PDB 6vjr Chain D Binding Site BS03

Receptor Information
>6vjr Chain D (length=500) Species: 436308 (Nitrosopumilus maritimus SCM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TIRSGDDYIESLRGRDLKVYLFGELVKEPVDHPMIRPSINAVAETYDLAL
REEALASADSSITGLKVNRFLHIAESAEDLVLQNKMQRKLGQNTGTCFQR
CVGMDAMNSLHSTTFEIDEKHGTDYHKRFLEFVKMVQQENLVIGGAMTDP
KGDRSKGPSEQDDPDLFTRIVDTDEKGVYVSGAKAHQTGCINSHWIILMP
TIRLTESDKDWAIVGAIPADAKGVTYIYGRQSCDTRSMEEGDIDDGNAKF
GGQEALIILDRVFIPWDKVFMHGEYEFASMLVERFTCYHRRSYVCKTGLG
DVLIGAAATIADYNGVPKVSHIKDKIIEMTHLNETIFAAGIASSHQGQKM
KSGVYLNDDMLAQVCKHNVTRFPYEISRLAQDIAGGLVVTLPSEKDFRHP
EAGPLLKKYLAGRKGVDVENRMRILRLIENMTLGRNAVGYLTESMHGAGS
PQAQRIQIQRQMQVGYKKNLAKNLAGITNDVEEPKESSEYFKRVFKTKDS
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 chain6vjr Chain D Residue 602 [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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PDB6vjr Structural adaptation of oxygen tolerance in a key archaeal carbon fixation enzyme
Resolution1.55 Å
Binding residue
(original residue number in PDB)		M153 T154 K157 R160 H192 Q193 T194 E449 H452 S456
Binding residue
(residue number reindexed from 1)		M147 T148 K151 R154 H186 Q187 T188 E443 H446 S450
Annotation score1
Enzymatic activity
Enzyme Commision number 5.3.3.3: vinylacetyl-CoA Delta-isomerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0016853 isomerase activity
GO:0046872 metal ion binding
GO:0050393 vinylacetyl-CoA delta-isomerase activity
GO:0051539 4 iron, 4 sulfur cluster binding

View graph for
Molecular Function
External links
PDB RCSB:6vjr, PDBe:6vjr, PDBj:6vjr
PDBsum6vjr
PubMed
UniProtA9A1Y2

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