Structure of PDB 3vpb Chain B Binding Site BS01

Receptor Information
>3vpb Chain B (length=282) Species: 273063 (Sulfurisphaera tokodaii str. 7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVVLIVDIVRQEEKLIAKALEENKVQYDIINVAQEPLPFNKALGRYDVA
IIRPVSMYRALYSSAVLEAAGVHTINSSDVINVCGDKILTYSKLYREGIP
IPDSIIALSAEAALKAYEQRGFPLIDKPPIGSWGRLVSLIRDVFEGKTII
EHRELMGNSALKAHIVQEYIQYKGRDIRCIAIGEELLGCYARNIPPNEWR
ANVALGGTPSNIEVDEKLKETVVKAVSIVHGEFVSIDILEHPNKGYVVNE
LNDVPEFKGFMVATNINVAQKLVEYIKENYSK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3vpb Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vpb Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus
Resolution1.8 Å
Binding residue
(original residue number in PDB)		K87 I125 K127 S132 G134 V137 Q167 Y169 I170 D176 R200 A201 N202 N249 E250
Binding residue
(residue number reindexed from 1)		K87 I125 K127 S132 G134 V137 Q167 Y169 I170 D176 R200 A201 N202 N249 E250
Annotation score5
Enzymatic activity
Enzyme Commision number 6.3.2.-
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042802 identical protein binding
GO:0043774 coenzyme F420-2 alpha-glutamyl ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006526 L-arginine biosynthetic process
GO:0009085 lysine biosynthetic process
GO:0036211 protein modification process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3vpb, PDBe:3vpb, PDBj:3vpb
PDBsum3vpb
PubMed23434852
UniProtQ970U6|ARGX_SULTO Glutamate--LysW ligase ArgX (Gene Name=argX)

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