6KWT | pdb_00006kwt

Crystal structure of Gre2 in complex with NADPH complex from Candida albicans

PDB DOI: https://doi.org/10.2210/pdb6KWT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candida albicans SC5314
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-09-08 Released: 2020-09-09
Deposition Author(s): Nguyen, G.T., Chang, J.H.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free:
0.211 (Depositor), 0.228 (DCC)
R-Value Work:
0.172 (Depositor), 0.203 (DCC)
R-Value Observed:
0.176 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of NADPH-Dependent Methylglyoxal Reductase Gre2 from Candida Albicans

Nguyen, G.T., Kim, S., Jin, H., Cho, D.H., Chun, H.S., Kim, W.K., Chang, J.H.

(2019) Crystals (Basel) 9

DOI: https://doi.org/10.3390/cryst9090471

Macromolecule Content

Total Structure Weight: 38.06 kDa
Atom Count: 2,684
Modeled Residue Count: 338
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylglyoxal reductase (NADPH-dependent)	A	338	Candida albicans SC5314	Mutation(s): 1 Gene Names: orf19.5611, CAALFM_C603240WA
UniProt
Find proteins for Q5ABT9 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore Q5ABT9 Go to UniProtKB: Q5ABT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ABT9
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free: 0.211 (Depositor), 0.228 (DCC)
R-Value Work: 0.172 (Depositor), 0.203 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.447	α = 90
b = 152.447	β = 90
c = 152.447	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2019R1A2C4069796

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2023-05-03
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection

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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.