5CVK

Structure of Xoo1075, a peptide deformyase from Xanthomonas oryzae pv. oryze, in complex with fragment 493

PDB DOI: https://doi.org/10.2210/pdb5CVK/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-07-27 Released: 2016-08-03
Deposition Author(s): Ngo, H.P.T., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.224
R-Value Work: 0.176
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of Xoo1075, a peptide deformyase from Xanthomonas oryzae pv.oryze, in complex with fragment 493

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

To be published.

Macromolecule Content

Total Structure Weight: 19.97 kDa
Atom Count: 1,532
Modelled Residue Count: 169
Deposited Residue Count: 171
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	171	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 0 Gene Names: def, XOO1075 EC: 3.5.1.88
UniProt
Find proteins for Q5H3Z2 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H3Z2 Go to UniProtKB: Q5H3Z2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5H3Z2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
56E Query on 56E Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	ethyl N-[(5-methylthiophen-3-yl)carbonyl]glycinate C₁₀ H₁₃ N O₃ S PMDIXZXNNWYFNT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], I [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]