PDBsum entry 5cpd

Hydrolase

PDB id: 5cpd

Contents

Protein chain

168 a.a.

Ligands

ACT

GOL

MET-ALA

Metals

_CD ×3

_NA ×2

Waters ×100

PDB id:

5cpd

Name:

Hydrolase

Title:

Methionine-alanine complex structure of peptide deformylase from xanthomonas oryzae pv. Oryzae

Structure:

Peptide deformylase. Chain: a. Fragment: unp residues 42-212. Synonym: pdf,polypeptide deformylase. Engineered: yes

Source:

Xanthomonas oryzae pv. Oryzae kacc10331. Organism_taxid: 291331. Strain: kacc10331. Gene: def, xoo1075. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.194 R-free: 0.247

Authors:

H.P.T.Ngo,L.W.Kang

Key ref:

H.P.T.Ngo and l.w.kang Methionine-Alanine complex structure of peptide defor from xanthomonas oryzae pv. Oryzae. To be published, .

Date:

21-Jul-15 Release date: 03-Aug-16

Protein chain

Q5H3Z2  (Q5H3Z2_XANOR) -  Peptide deformylase from Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)

Seq: 212 a.a.

Struc: 168 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.5.1.88 - peptide deformylase.
• Reaction: N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] + formate

N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] (Bound ligand (Het Group name = ACT) matches with 75.00% similarity) + formate

• Cofactor: Fe(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site