4F8Y | pdb_00004f8y

Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans

PDB DOI: https://doi.org/10.2210/pdb4F8Y/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus mutans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-05-18 Released: 2012-06-06
Deposition Author(s): Wang, Z., Li, L., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.183 (Depositor), 0.170 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans

Wang, Z., Li, L., Su, X.-D.

To be published.

Macromolecule Content

Total Structure Weight: 95.14 kDa
Atom Count: 6,966
Modeled Residue Count: 768
Deposited Residue Count: 784
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH Quinone Oxidoreductase	A, B, C, D	196	Streptococcus mutans	Mutation(s): 0 Gene Names: SMU_1420 EC: 1.6.5.2
UniProt
Find proteins for Q8DTD1 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTD1 Go to UniProtKB: Q8DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DTD1
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 E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
VK3 Query on VK3 Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	MENADIONE C₁₁ H₈ O₂ MJVAVZPDRWSRRC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]