9HDM | pdb_00009hdm

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), 0.192 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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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
Modeled Residue Count: 687
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SHQ5
Sequence Annotations Expand
Reference Sequence

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 H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	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 F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	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]