9GA1 | pdb_00009ga1

Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus

PDB DOI: https://doi.org/10.2210/pdb9GA1/pdb

Classification: LIPID TRANSPORT
Organism(s): Bdellovibrio bacteriovorus HD100
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-26 Released: 2025-07-09
Deposition Author(s): Parr, R.J., Lovering, A.L.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.239 (Depositor), 0.241 (DCC)
R-Value Work:
0.198 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A porin-like protein used by bacterial predator defines a wider lipid-trapping superfamily

Parr, R.J., Lovering, A.L.

(2025) Nat Commun

DOI: https://doi.org/10.1038/s41467-025-61633-0

Macromolecule Content

Total Structure Weight: 185.07 kDa
Atom Count: 13,197
Modeled Residue Count: 1,665
Deposited Residue Count: 1,665
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major outer membrane protein	A, B, C, D, E	333	Bdellovibrio bacteriovorus HD100	Mutation(s): 0 Gene Names: Bd0427
UniProt
Find proteins for Q6MQN4 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MQN4 Go to UniProtKB: Q6MQN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6MQN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain U [auth D] SDF format, chain Z [auth E] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Z [auth E]	F [auth A], L [auth B], O [auth C], U [auth D], Z [auth E]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth D] Focus chain Z [auth E] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth D] Focus chain Z [auth E]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain X [auth D]	BA [auth E], J [auth A], N [auth B], X [auth D]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain BA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain X [auth D]
OC9 Query on OC9 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain K [auth A] SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D]	AA [auth E], K [auth A], R [auth C], W [auth D]	OCTAN-1-OL C₈ H₁₈ O KBPLFHHGFOOTCA-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain K [auth A] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain K [auth A] Focus chain R [auth C] Focus chain W [auth D]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	G [auth A] H [auth A] I [auth A] M [auth B] P [auth C] G [auth A], H [auth A], I [auth A], M [auth B], P [auth C], Q [auth C], S [auth D], T [auth D], V [auth D], Y [auth E]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth D] Focus chain Y [auth E]