Structure of PDB 2xd4 Chain A Binding Site BS03

Receptor Information
>2xd4 Chain A (length=421) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNVLIIGKGGREHTLAWKAAQSSLVENVFAAPGNDGMAASAQLVNIEESD
HAGLVSFAKQNQVGLTIVGPEVPLIEGLVDEFEKAGLHVFGPSKAAAIIE
GSKQFAKDLMKKYDIPTAEYETFTSFDEAKAYVQEKGAPIVIKADGLAAG
KGVTVAMTEEEAIACLHDFLEDEKFGDASASVVIEEYLSGEEFSLMAFVK
GEKVYPMVIAQDHKRAFDGDKGPNTGGMGAYSPVPQISEETVRHAVETIV
KPAAKAMVQEGRSFTGVLYAGLMLTENGSKVIEFNARFGDPETQVVLPRM
ESDLVQVLLDLLDDKEVDLRWKDTAAVSVVLASEGYPESYAKGTPIGSLA
AETEQVVVFHAGTKAEGGEFVTNGGRVANVTAFDETFEAARDRVYKAVDE
IFKPGLFFRKDIGARALKAAQ
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 chain2xd4 Chain A Residue 461 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xd4 Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase
Resolution2.65 Å
Binding residue
(original residue number in PDB)		K103 V141 K143 G150 V153 E185 L188 E192 K214 I282 E283
Binding residue
(residue number reindexed from 1)		K103 V141 K143 G150 V153 E185 L188 E192 K214 I282 E283
Annotation score5
Enzymatic activity
Enzyme Commision number 6.3.4.13: phosphoribosylamine--glycine ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004637 phosphoribosylamine-glycine ligase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0006189 'de novo' IMP biosynthetic process
GO:0009113 purine nucleobase biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:2xd4, PDBe:2xd4, PDBj:2xd4
PDBsum2xd4
PubMed
UniProtP12039|PUR2_BACSU Phosphoribosylamine--glycine ligase (Gene Name=purD)

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