Structure of PDB 3mf1 Chain B Binding Site BS02

Receptor Information

>3mf1 Chain B (length=275) Species: 224911 (Bradyrhizobium diazoefficiens USDA 110)

DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRF
PPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTT
SLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLD
RLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYALKFE
LLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRL
AVAMFHTHGTDLSAWPAKVRDILGL

Ligand information

• Ligand ID: G5A
• InChI: InChI=1S/C12H17N7O7S/c13-1-6(20)18-27(23,24)25-2-5-8(21)9(22)12(26-5)19-4-17-7-10(14)15-3-16-11(7)19/h3-5,8-9,12,21-22H,1-2,13H2,(H,18,20)(H2,14,15,16)/t5-,8-,9-,12-/m1/s1
• InChIKey: AMWPZASLDLLQFT-JJNLEZRASA-N
• SMILES:
  ACDLabs 11.02: O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)CN
  CACTVS 3.352: NCC(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)CN)O)O)N
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)CN)O)O)N
  CACTVS 3.352: NCC(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
• Formula: C12 H17 N7 O7 S
• Name: 5'-O-(glycylsulfamoyl)adenosine
• ChEMBL: CHEMBL1163073
• ZINC: ZINC000014967098
• PDB chain: 3mf1 Chain B Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3mf1 Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): R159 E161 L169 F172 M174 E176 K235 A250 C251 S253 C279 A281 G283 R286
• Binding residue (residue number reindexed from 1): R142 E144 L152 F155 M157 E159 K198 A213 C214 S216 C242 A244 G246 R249
• Annotation score: 3

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 K198 A213 S216 C242 R249
• 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

External links

• PDB: RCSB:3mf1, PDBe:3mf1, PDBj:3mf1
• PDBsum: 3mf1
• PubMed: 20663952
• UniProt: Q89VT8|AACL1_BRADU Amino acid--[acyl-carrier-protein] ligase 1 (Gene Name=bll0957)