4WXL | pdb_00004wxl

Crystal structure of a peptide deformylase from Haemophilus influenzae complex with Actinonin

PDB DOI: https://doi.org/10.2210/pdb4WXL/pdb

Classification: HYDROLASE
Organism(s): Haemophilus influenzae 86-028NP
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-14 Released: 2015-11-18
Deposition Author(s): Kishor, C., Addlagatta, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a peptide deformylase from Haemophilus influenzae complex with Actinonin

Kishor, C., Addlagatta, A.

To be published.

Macromolecule Content

Total Structure Weight: 78.11 kDa
Atom Count: 5,420
Modeled Residue Count: 655
Deposited Residue Count: 676
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, B, C, D	169	Haemophilus influenzae 86-028NP	Mutation(s): 0 Gene Names: def, NTHI0725 EC: 3.5.1.88
UniProt
Find proteins for Q4QMV6 (Haemophilus influenzae (strain 86-028NP)) Explore Q4QMV6 Go to UniProtKB: Q4QMV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4QMV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BB2 Query on BB2 Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]