Structure of PDB 6jf4 Chain A Binding Site BS02

Receptor Information

>6jf4 Chain A (length=148) Species: 470 (Acinetobacter baumannii)

SVVLPVAKRGEDILKLIAAPVSANELNSNWLYQLADAMHATMLERNGVGI
AAPQVYISKRVIIVASPEMNAVVMVNPEILEFSSETCLGEEGCLSVPDER
GQVERAEMVKVKYLTLQGEAVETIFHGFPARIVQHEVDHLNGILFVER

Ligand information

• Ligand ID: K1U
• InChI: InChI=1S/C19H18O4S/c20-17(15-9-5-2-6-10-15)13-24-19(23)16(12-18(21)22)11-14-7-3-1-4-8-14/h1-10,16H,11-13H2,(H,21,22)/t16-/m1/s1
• InChIKey: XBDWLLDIBQGWMW-MRXNPFEDSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)C[C@H](CC(=O)O)C(=O)SCC(=O)c2ccccc2
  CACTVS 3.385: OC(=O)C[C@@H](Cc1ccccc1)C(=O)SCC(=O)c2ccccc2
  ACDLabs 12.01: OC(CC(Cc1ccccc1)C(=O)SCC(=O)c2ccccc2)=O
  CACTVS 3.385: OC(=O)C[CH](Cc1ccccc1)C(=O)SCC(=O)c2ccccc2
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)CC(CC(=O)O)C(=O)SCC(=O)c2ccccc2
• Formula: C19 H18 O4 S
• Name: (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid
• PDB chain: 6jf4 Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6jf4 K1U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): N47 G48 V49 G50 Q55 E101 G102 C103 L104 R110 F138 H145 E146
• Binding residue (residue number reindexed from 1): N46 G47 V48 G49 Q54 E91 G92 C93 L94 R100 F128 H135 E136
• 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 C93 L94 H135 E136 H139
• 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:6jf4, PDBe:6jf4, PDBj:6jf4
• PDBsum: 6jf4
• UniProt: A0A098SKQ8