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), 0.194 (DCC)
R-Value Work:
0.141 (Depositor), 0.153 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.194 (DCC)
R-Value Work: 0.141 (Depositor), 0.153 (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

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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

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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.