Structure of PDB 5jf2 Chain A Binding Site BS04

Receptor Information

>5jf2 Chain A (length=203) Species: 1311 (Streptococcus agalactiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AAIDKLVKASHLIDMNDIIREGNPTLRKVAEEVTFPLSEKEEILGEKMMQ
FLKHSQDPIMAEKLGLRGGVGLAAPQLDISKRIIAVLVPNVEDAQGNPPK
EAYSLQEVMYNPKVVSHSVQDAALSDGEGCLSVDREVPGYVVRHARVTIE
YFDKTGEKHRLKLKGYNSIVVQHEIDHIDGIMFYDRINEKNPFAVKEGLL
ILE

Ligand information

Ligand ID

InChI

InChI=1S/Zn/q+2

InChIKey

PTFCDOFLOPIGGS-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	[Zn++]
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Zn+2]

Formula

Name

ZINC ION

PDB chain

5jf2 Chain A Residue 310 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	5jf2 A unique peptide deformylase platform to rationally design and challenge novel active compounds.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	E43 E47
Binding residue (residue number reindexed from 1)	E42 E46
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	G72 Q77 C131 L132 H174 E175 H178
Catalytic site (residue number reindexed from 1)	G71 Q76 C130 L131 H173 E174 H177
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

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:5jf2, PDBe:5jf2, PDBj:5jf2
PDBsum	5jf2
PubMed	27762275
UniProt	Q8E378\|DEF_STRA3 Peptide deformylase (Gene Name=def)

[Back to BioLiP]