9KNP | pdb_00009knp

X-ray structure of Pyrococcus horikoshii OT3 alcohol dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb9KNP/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-19 Released: 2025-11-05
Deposition Author(s): Kamitori, S., Nakamura, N.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.253 (Depositor), 0.258 (DCC)
R-Value Work:
0.218 (Depositor), 0.226 (DCC)

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

X-ray structure of Pyrococcus horikoshii OT3 alcohol dehydrogenase

Kamitori, S., Nakamura, N.

To be published.

Macromolecule Content

Total Structure Weight: 86.55 kDa
Atom Count: 6,392
Modeled Residue Count: 751
Deposited Residue Count: 766
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
375aa long hypothetical alchol dehydrogenase	A, B	383	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: PH0743
UniProt
Find proteins for O58517 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58517 Go to UniProtKB: O58517
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58517
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
1BO (Subject of Investigation/LOI) Query on 1BO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
NI (Subject of Investigation/LOI) Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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]