Structure of PDB 3mf2 Chain B Binding Site BS02

Receptor Information
>3mf2 Chain B (length=296) Species: 224911 (Bradyrhizobium diazoefficiens USDA 110) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRF
PPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTT
SLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLD
RLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPF
FGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGI
QDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGLQ
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain3mf2 Chain B Residue 1010 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mf2 Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis
Resolution2.15 Å
Binding residue
(original residue number in PDB)		R159 L169 F172 K235 A250 C251 M252 G283 R286
Binding residue
(residue number reindexed from 1)		R142 L152 F155 K218 A233 C234 M235 G266 R269
Annotation score5
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) C114 R142 E144 R151 E159 K218 A233 S236 C262 R269
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:3mf2, PDBe:3mf2, PDBj:3mf2
PDBsum3mf2
PubMed20663952
UniProtQ89VT8|AACL1_BRADU Amino acid--[acyl-carrier-protein] ligase 1 (Gene Name=bll0957)

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