9TPM | pdb_00009tpm

Structure of LolB from Porphyromonas gingivalis

PDB DOI: https://doi.org/10.2210/pdb9TPM/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Porphyromonas gingivalis A7A1-28
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-12-18 Released: 2026-02-18
Deposition Author(s): Jaiman, D., Persson, K.
Funding Organization(s): Swedish Research Council, Kempe Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.278 (Depositor), 0.277 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: in silico
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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 of LolB from Porphyromonas gingivalis

Jaiman, D., Persson, K., Hasegawa, Y., Hirohata, M.

To be published.

Macromolecule Content

Total Structure Weight: 32.6 kDa
Atom Count: 2,043
Modeled Residue Count: 236
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4292 domain-containing protein	A	274	Porphyromonas gingivalis A7A1-28	Mutation(s): 4 Gene Names: PG_0955
UniProt
Find proteins for Q7MVT4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVT4 Go to UniProtKB: Q7MVT4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MVT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4G Query on P4G Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A], N [auth A]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	O [auth A], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions 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 F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]