5U1H

Crystal structure of the C-terminal peptidoglycan binding domain of OprF (PA1777) from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb5U1H/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-28 Released: 2017-01-11
Deposition Author(s): Watanabe, N., Stogios, P.J., Skarina, T., Wawrzak, Z., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.200
R-Value Work: 0.166
R-Value Observed: 0.167

Starting Model: experimental
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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 the C-terminal peptidoglycan binding domain of OprF (PA1777) from Pseudomonas aeruginosa

Watanabe, N.

To be published.

Macromolecule Content

Total Structure Weight: 56.28 kDa
Atom Count: 4,718
Modelled Residue Count: 490
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane porin F	A, B, C, D	123	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: oprF, PA1777
UniProt
Find proteins for P13794 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P13794 Go to UniProtKB: P13794
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13794
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7QA Query on 7QA Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain E [auth A]	E [auth A], H [auth B], P [auth C], U [auth D]	(2R,6S)-2-amino-6-(carboxyamino)-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoic acid C₁₁ H₁₉ N₃ O₇ HUCJTZSCCQLPOD-QYNIQEEDSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain U [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain L [auth B] SDF format, chain T [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B]	F [auth A], N [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth D]	G [auth A], O [auth B], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain O [auth B] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth B] Focus chain X [auth D]