2R6H

Crystal structure of the domain comprising the NAD binding and the FAD binding regions of the NADH:ubiquinone oxidoreductase, Na translocating, F subunit from Porphyromonas gingivalis

PDB DOI: https://doi.org/10.2210/pdb2R6H/pdb

Classification: OXIDOREDUCTASE
Organism(s): Porphyromonas gingivalis W83
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-05 Released: 2007-09-11
Deposition Author(s): Kim, Y., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.271
R-Value Work: 0.215
R-Value Observed: 0.221

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 Domain Comprising the Regions Binding NAD and FAD from the NADH:Ubiquinone Oxidoreductase, Na Translocating, F Subunit from Porphyromonas gingivalis.

Kim, Y., Mulligan, R., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 139.48 kDa
Atom Count: 9,919
Modelled Residue Count: 1,144
Deposited Residue Count: 1,160
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase, Na translocating, F subunit	A, B, C, D	290	Porphyromonas gingivalis W83	Mutation(s): 0 Gene Names: nqrF, PG_2177 EC: 1.6.5
UniProt
Find proteins for Q7MT22 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MT22 Go to UniProtKB: Q7MT22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MT22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D]	H [auth A], K [auth B], P [auth C], S [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D]