7RK5 | pdb_00007rk5

Mannitol-2-dehydrogenase bound to NADH from Aspergillus fumigatus

PDB DOI: https://doi.org/10.2210/pdb7RK5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-22 Released: 2022-07-27
Deposition Author(s): Nguyen, S., Bruning, J.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.249 (Depositor), 0.253 (DCC)
R-Value Work:
0.190 (Depositor), 0.195 (DCC)
R-Value Observed:
0.193 (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

Targeting the Mannitol Biosynthesis Pathway in Aspergillus fumigatus: Characterisation and Inhibition of Mannitol-2-Dehydrogenase

Nguyen, S., Jovcevski, B., Pukala, T.L., Bruning, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 116.36 kDa
Atom Count: 8,340
Modeled Residue Count: 990
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannitol 2-dehydrogenase	A [auth B], B [auth A]	510	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: AFUA_4G14450 EC: 1.1.1.67
UniProt
Find proteins for Q4WQY4 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WQY4 Go to UniProtKB: Q4WQY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4WQY4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.249 (Depositor), 0.253 (DCC)
R-Value Work: 0.190 (Depositor), 0.195 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.883	α = 90
b = 71.289	β = 101.15
c = 69.157	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2023-10-18
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.