5CWY | pdb_00005cwy

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryze pv oryzae, in complex with fragment 83

PDB DOI: https://doi.org/10.2210/pdb5CWY/pdb

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

Deposited: 2015-07-28 Released: 2016-08-03
Deposition Author(s): Ngo, H.P.T., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

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 deformylase from Xanthomonas oryze pv oryzae, in complex with fragment 83

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

To be published.

Macromolecule Content

Total Structure Weight: 19.68 kDa
Atom Count: 1,452
Modeled Residue Count: 168
Deposited Residue Count: 171
Unique protein chains: 1

Macromolecules

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(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
4WL Query on 4WL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	4H-THIENO[3,2-B]PYROLE-5-CARBOXYLIC ACID C₇ H₅ N O₂ S PMHDSACGRKBACK-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] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]