Structure of PDB 2vpy Chain A Binding Site BS02

Receptor Information
>2vpy Chain A (length=734) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APWYAQEVKSVYQICEGCFWRCGIVAHAVGNRVYKVEGYEANPKSRGRLC
PRGQGAPQTTYDPDRLKRPLIRVEGSQRGEGKYRVATWEEALDHIAKKML
EIREKYGPEAIAFFGHGTGDYWFVDFLPAAWGSPNAAKPSVSLCTAPREV
ASQWVFGRPIGGHEPIDWENARYIVLIGHHIGEDTHNTQLQDFALALKNG
AKVVVVDPRFSTAAAKAHRWLPIKPGTDTALLLAWIHVLIYEDLYDKEYV
AKYTVGFEELKAHVKDFTPEWAEKHTEIPAQVIREVAREMAAHKPRAVLP
PTRHNVWYGDDTYRVMALLYVNVLLGNYGRPGGFYIAQSPYLEKYPLPPL
PLEPAAGGCSGPSGGDHEPEGFKPRADKGKFFARSTAIQELIEPMITGEP
YPIKGLFAYGINLFHSIPNVPRTKEALKNLDLYVAIDVLPQEHVMWADVI
LPEATYLERYDDFVLVAHKTPFIQLRTPAHEPLFDTKPGWWIARELGLRL
GLEQYFPWKTIEEYLETRLQSLGLDLETMKGMGTLVQRGKPWLEDWEKEG
RLPFGTASGKIELYCQRFKEAGHQPLPVFTPPEEPPEGFYRLLYGRSPVH
TFARTQNNWVLMEMDPENEVWIHKEEAKRLGLKEGDYVMLVNQDGVKEGP
VRVKPTARIRKDCVYIVHGFGHKAPLMRLAHGRGASDNYLQTRYKLDPIS
GGAGLRVNFVRLEKAERPRLPSLTGLAKRPFDER
Ligand information
Ligand IDMGD
InChIInChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
InChIKeyVQAGYJCYOLHZDH-ILXWUORBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O
CACTVS 3.341NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
FormulaC20 H26 N10 O13 P2 S2
Name2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE;
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000195757106
PDB chain2vpy Chain A Residue 1765 [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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PDB2vpy Molecular Mechanism of Energy Conservation in Polysulfide Respiration.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
H145 L172 C173 G439 I440 N441 H444 S445 I465 D466 Q470 E482 R488 Y623 R625 F631 A632 R633 H697 D716 N717
Binding residue
(residue number reindexed from 1)
H116 L143 C144 G410 I411 N412 H415 S416 I436 D437 Q441 E453 R459 Y594 R596 F602 A603 R604 H668 D687 N688
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R81 H145 D149 K167 C173 T174 R332 Y364 P369 Y370 P380
Catalytic site (residue number reindexed from 1) R52 H116 D120 K138 C144 T145 R303 Y335 P340 Y341 P351
Enzyme Commision number 1.-.-.-
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding

View graph for
Molecular Function
External links
PDB RCSB:2vpy, PDBe:2vpy, PDBj:2vpy
PDBsum2vpy
PubMed18536726
UniProtQ72LA4

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