7YMB | pdb_00007ymb

Structure of Alcohol dehydrogenase from Candida glabrata(CgADH)complexed with NADPH

PDB DOI: https://doi.org/10.2210/pdb7YMB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nakaseomyces glabratus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-28 Released: 2023-08-02
Deposition Author(s): Sun, Z.W., Liu, Y.F., Xu, G.C., Ni, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.220 (Depositor), 0.221 (DCC)
R-Value Work:
0.185 (Depositor), 0.192 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

rational desigen of CgADH from Candida glabrata for stereocomplementary reduction of azacyclone.

Sun, Z.W., Ni, Y., Xu, G.C.

To be published.

Macromolecule Content

Total Structure Weight: 39.81 kDa
Atom Count: 3,038
Modeled Residue Count: 343
Deposited Residue Count: 351
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-dependent methylglyoxal reductase GRE2	A	351	Nakaseomyces glabratus	Mutation(s): 0
UniProt
Find proteins for A0A0W0CJZ6 (Candida glabrata) Explore A0A0W0CJZ6 Go to UniProtKB: A0A0W0CJZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0W0CJZ6
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: 1.80 Å
R-Value Free: 0.220 (Depositor), 0.221 (DCC)
R-Value Work: 0.185 (Depositor), 0.192 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.644	α = 90
b = 48.322	β = 96.63
c = 70.475	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22078127

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection
Version 1.2: 2026-03-04
Changes: Refinement description, Structure summary

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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.