46AQ | pdb_000046aq

Crystal structure of the diaminopimelate dehydrogenase from Pyrococcus sp. in its apo form

PDB DOI: https://doi.org/10.2210/pdb46AQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus sp.
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-09-16 Released: 2026-11-11
Deposition Author(s): Matyuta, I.O., Bezsudnova, E.Y., Popov, V.O., Boyko, K.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.314 (Depositor), 0.319 (DCC)
R-Value Work:
0.286 (Depositor), 0.287 (DCC)
R-Value Observed:
0.289 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 46AQ

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

Literature

D-amino acid dehydrogenase from archaeon Pyrococcus sp. stereoselectively aminates alpha-keto acids using NADH or NADPH

Rudina, J.V., Matyuta, I.O., Bakunova, A.K., Boyko, K.M., Popov, V.O., Bezsudnov, E.Y.

To be published.

Macromolecule Content

Total Structure Weight: 105.62 kDa
Atom Count: 6,797
Modeled Residue Count: 911
Deposited Residue Count: 933
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate dehydrogenase	A, B [auth C], C [auth E]	311	Pyrococcus sp.	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth C] SDF format, chain F [auth E] MOL2 format, chain D [auth A] MOL2 format, chain E [auth C] MOL2 format, chain F [auth E] mmCIF format, chain D [auth A] mmCIF format, chain E [auth C] mmCIF format, chain F [auth E]	D [auth A], E [auth C], F [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth C] Focus chain F [auth E] Interactions & Density Focus chain D [auth A] Focus chain E [auth C] Focus chain F [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.314 (Depositor), 0.319 (DCC)
R-Value Work: 0.286 (Depositor), 0.287 (DCC)
R-Value Observed: 0.289 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.278	α = 90
b = 122.232	β = 96.21
c = 83.407	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Bezsudnova, E.Y.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release