7W1W | pdb_00007w1w

NADPH-bound AKR4C17 mutant F291D

PDB DOI: https://doi.org/10.2210/pdb7W1W/pdb

Classification: OXIDOREDUCTASE
Organism(s): Echinochloa colona
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-11-21 Released: 2022-07-06
Deposition Author(s): Li, H., Yang, Y., Hu, Y., Chen, C.-C., Huang, J.-W., Min, J., Dai, L., Guo, R.-T.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.185 (Depositor), 0.190 (DCC)
R-Value Work:
0.141 (Depositor), 0.150 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural analysis and engineering of aldo-keto reductase from glyphosate-resistant Echinochloa colona

Li, H., Yang, Y., Hu, Y., Chen, C.C., Huang, J.W., Min, J., Dai, L., Guo, R.T.

(2022) J Hazard Mater 436: 129191

DOI: https://doi.org/10.1016/j.jhazmat.2022.129191

Macromolecule Content

Total Structure Weight: 72.11 kDa
Atom Count: 5,855
Modeled Residue Count: 617
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AKR4-2	A, B	321	Echinochloa colona	Mutation(s): 1
UniProt
Find proteins for A0A5J6VLZ7 (Echinochloa colona) Explore A0A5J6VLZ7 Go to UniProtKB: A0A5J6VLZ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5J6VLZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.185 (Depositor), 0.190 (DCC)
R-Value Work: 0.141 (Depositor), 0.150 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.879	α = 90
b = 81.558	β = 104.25
c = 68.896	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	2021YFC2100300

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.