Structure of PDB 2vpy Chain E Binding Site BS03

Receptor Information
>2vpy Chain E (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 E Residue 1766 [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)
R81 H208 H209 D213 T214 H215 V235 D236 P237 R238 D257 T331 R332 H333 W336 Y337 L622 R625 P627 H629 T630 F631 R735
Binding residue
(residue number reindexed from 1)
R52 H179 H180 D184 T185 H186 V206 D207 P208 R209 D228 T302 R303 H304 W307 Y308 L593 R596 P598 H600 T601 F602 R706
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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