Structure of PDB 6jf5 Chain B Binding Site BS02

Receptor Information

>6jf5 Chain B (length=158) Species: 470 (Acinetobacter baumannii)

SVVLPVAKRGEDILKLIAAPVSANELNSNWLYQLADAMHATMLERNGVGI
AAPQVYISKRVIIVASRPNPRYPDAPEMNAVVMVNPEILEFSSETCLGEE
GCLSVPDERGQVERAEMVKVKYLTLQGEAVETIFHGFPARIVQHEVDHLN
GILFVERI

Ligand information

• Ligand ID: K2U
• InChI: InChI=1S/C18H20O3S/c19-17(20)12-16(11-14-7-3-1-4-8-14)18(21)22-13-15-9-5-2-6-10-15/h1-10,16,18,21H,11-13H2,(H,19,20)/t16-,18-/m1/s1
• InChIKey: OBXQOECJZPGJTO-SJLPKXTDSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)CC(CC(=O)O)C(O)SCc2ccccc2
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)C[C@H](CC(=O)O)[C@H](O)SCc2ccccc2
  CACTVS 3.385: O[C@H](SCc1ccccc1)[C@@H](CC(O)=O)Cc2ccccc2
  CACTVS 3.385: O[CH](SCc1ccccc1)[CH](CC(O)=O)Cc2ccccc2
• Formula: C18 H20 O3 S
• Name: (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid
• PDB chain: 6jf5 Chain B Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6jf5 K2U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G48 V49 Q55 E101 G102 C103 L104 R110 F138 H145 E146
• Binding residue (residue number reindexed from 1): G47 V48 Q54 E100 G101 C102 L103 R109 F137 H144 E145
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G50 Q55 C103 L104 H145 E146 H149
• Catalytic site (residue number reindexed from 1): G49 Q54 C102 L103 H144 E145 H148
• Enzyme Commision number: 3.5.1.88: peptide deformylase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0042586 peptide deformylase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0018206 peptidyl-methionine modification

External links

• PDB: RCSB:6jf5, PDBe:6jf5, PDBj:6jf5
• PDBsum: 6jf5
• UniProt: A0A098SKQ8