8JTO | pdb_00008jto

Outer membrane porin of Burkholderia pseudomallei (BpsOmp38) in complex with ceftazidime

PDB DOI: https://doi.org/10.2210/pdb8JTO/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Burkholderia pseudomallei
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-06-22 Released: 2024-06-26
Deposition Author(s): Bunkum, P., Aunkham, A., Bert van den, B., Robinson, R.C., Suginta, W.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.223 (Depositor), 0.224 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure and function of outer membrane protein from Burkholderia pseudomallei (BpsOmp38)

Bunkum, P., Aunkham, A., Bert van den, B., Robinson, R.C., Suginta, W.

To be published.

Macromolecule Content

Total Structure Weight: 40.82 kDa
Atom Count: 2,759
Modeled Residue Count: 343
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane porin (Fragment)	A	360	Burkholderia pseudomallei	Mutation(s): 0 Gene Names: omp38 Membrane Entity: Yes
UniProt
Find proteins for A0A069BCC8 (Burkholderia pseudomallei) Explore A0A069BCC8 Go to UniProtKB: A0A069BCC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A069BCC8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C8E (Subject of Investigation/LOI) Query on C8E Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-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 F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [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 F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]