4QGS | pdb_00004qgs

Substrate and cofactor-free form of the Aldehyde Reductase YqhD from E. coli.

PDB DOI: https://doi.org/10.2210/pdb4QGS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Mutation(s): No

Deposited: 2014-05-24 Released: 2015-05-06
Deposition Author(s): LaMattina, J.W., Kapoor, S., Lanzilotta, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4QGS

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

Literature

Open form of E. coli YqhD

LaMattina, J.W., Kapoor, S., Gouvea, I., Slovic, A., Lanzilotta, W.N.

To be published.

Macromolecule Content

Total Structure Weight: 43.54 kDa
Atom Count: 3,214
Modeled Residue Count: 380
Deposited Residue Count: 398
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase YqhD	A	398	Escherichia coli K-12	Mutation(s): 0 Gene Names: yqhD, b3011, JW2978 EC: 1.1.1 (PDB Primary Data), 1.1.1.2 (UniProt)
UniProt
Find proteins for Q46856 (Escherichia coli (strain K12)) Explore Q46856 Go to UniProtKB: Q46856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46856
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.186 (Depositor), 0.187 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.402	α = 90
b = 68.441	β = 118.46
c = 66.602	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-05-06

Deposition Author(s):

LaMattina, J.W.

Lanzilotta, W.N.

Revision History (Full details and data files)

Version 1.0: 2015-05-06
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.