6ZHV | pdb_00006zhv

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic

PDB DOI: https://doi.org/10.2210/pdb6ZHV/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2020-06-23 Released: 2021-05-05
Deposition Author(s): Sousa, C.F., Morais-Cabral, J., Gameiro, P.
Funding Organization(s): Foundation for Science and Technology (FCT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.233 (Depositor), 0.236 (DCC)
R-Value Work:
0.198 (Depositor), 0.202 (DCC)
R-Value Observed:
0.199 (Depositor)

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 OmpF porin soaked in ciprofloxacin metaloantibiotic

Sousa, C.F., Morais-Cabral, J., Gameiro, P.

To be published.

Macromolecule Content

Total Structure Weight: 120.28 kDa
Atom Count: 8,226
Modeled Residue Count: 1,022
Deposited Residue Count: 1,086
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane porin F	A [auth B], B [auth A], C	362	Escherichia coli K-12	Mutation(s): 0 Gene Names: ompF, cmlB, coa, cry, tolF, b0929, JW0912 Membrane Entity: Yes
UniProt
Find proteins for P02931 (Escherichia coli (strain K12)) Explore P02931 Go to UniProtKB: P02931
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QLB Query on QLB Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain J [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain J [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain J [auth B]	J [auth B] P [auth A] Q [auth A] V [auth C] W [auth C] J [auth B], P [auth A], Q [auth A], V [auth C], W [auth C], X [auth C], Y [auth C]	2-[2-(2-octoxyethoxy)ethoxy]ethanol C₁₄ H₃₀ O₄ XIVLVYLYOMHUGB-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain J [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain K [auth A] SDF format, chain D [auth B] MOL2 format, chain R [auth C] MOL2 format, chain K [auth A] MOL2 format, chain D [auth B] mmCIF format, chain R [auth C] mmCIF format, chain K [auth A] mmCIF format, chain D [auth B]	D [auth B], K [auth A], R [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain K [auth A] Focus chain R [auth C] Interactions & Density Focus chain D [auth B] Focus chain K [auth A] Focus chain R [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] G [auth B] H [auth B] I [auth B] E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], L [auth A], M [auth A], N [auth A], O [auth A], S [auth C], T [auth C], U [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]