Structure of PDB 3pzc Chain A Binding Site BS02

Receptor Information
>3pzc Chain A (length=296) Species: 375 (Bradyrhizobium japonicum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALR
FPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWT
TSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHL
DRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDP
FFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWG
IQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL
Ligand information
Ligand IDGAP
InChIInChI=1S/C12H17N6O8P/c13-1-6(19)26-27(22,23)24-2-5-8(20)9(21)12(25-5)18-4-17-7-10(14)15-3-16-11(7)18/h3-5,8-9,12,20-21H,1-2,13H2,(H,22,23)(H2,14,15,16)/t5-,8-,9-,12-/m1/s1
InChIKeyHROXHMRQKGGIFT-JJNLEZRASA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P]([O-])(=O)OC(=O)C[NH3+])[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)([O-])OC(=O)C[NH3+])O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P]([O-])(=O)OC(=O)C[NH3+])[C@@H](O)[C@H]3O
ACDLabs 10.04[O-]P(=O)(OC(=O)C[NH3+])OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)([O-])OC(=O)C[NH3+])O)O)N
FormulaC12 H17 N6 O8 P
NameGLYCYL-ADENOSINE-5'-PHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain3pzc Chain A Residue 1001 [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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PDB3pzc Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R159 L169 F172 M174 E176 K235 A250 C251 M252 S253 G283 R286
Binding residue
(residue number reindexed from 1)		R143 L153 F156 M158 E160 K219 A234 C235 M236 S237 G267 R270
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) C131 R159 E161 R168 E176 K235 A250 S253 C279 R286
Catalytic site (residue number reindexed from 1) C115 R143 E145 R152 E160 K219 A234 S237 C263 R270
Enzyme Commision number 6.2.1.n2: amino acid--[acyl-carrier-protein] ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3pzc, PDBe:3pzc, PDBj:3pzc
PDBsum3pzc
PubMed
UniProtQ89VT8|AACL1_BRADU Amino acid--[acyl-carrier-protein] ligase 1 (Gene Name=bll0957)

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