9HDM

Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa in complex with thymidine

PDB DOI: https://doi.org/10.2210/pdb9HDM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Neurospora crassa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-12 Released: 2025-02-26
Deposition Author(s): Friedrich, F., Genz, F., Einsle, O., Mueller, M., Fessner, N.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Identification and Characterization of Pyrimidine Nucleoside 2'-Hydroxylase

Genz, F., Friedrich, F., Lonarz, C., Einsle, O., Jung, M., Muller, M., Fessner, N.D.

(2025) ACS Catal

DOI: https://doi.org/10.1021/acscatal.4c07764

Macromolecule Content

Total Structure Weight: 85.8 kDa
Atom Count: 6,017
Modelled Residue Count: 687
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clavaminate synthase-like protein	A, B	390	Neurospora crassa	Mutation(s): 0 Gene Names: NCU02560
UniProt
Find proteins for Q7SHQ5 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q7SHQ5 Go to UniProtKB: Q7SHQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SHQ5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THM (Subject of Investigation/LOI) Query on THM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	THYMIDINE C₁₀ H₁₄ N₂ O₅ IQFYYKKMVGJFEH-XLPZGREQSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
BU3 Query on BU3 Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]