44YD | pdb_000044yd

Crystal structure of D-lactate dehydrogenase from Lacticaseibacillus rhamnosus in its apoform

PDB DOI: https://doi.org/10.2210/pdb44YD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lacticaseibacillus rhamnosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-08-17 Released: 2026-11-04
Deposition Author(s): Matyuta, I.O., Pometun, A.A., Loginova, A.A., Popov, V.O., Boyko, K.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.324 (Depositor), 0.324 (DCC)
R-Value Work:
0.249 (Depositor), 0.249 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of D-lactate dehydrogenase from Lacticaseibacillus rhamnosus in its apoform

Loginova, A.A., Kotina, A.S., Chachin, P.V., Mordkovich, N.N., Okorokova, N.A., Kleymenov, S.Y., Sokolovskaya, A.A., Boyko, K.M., Matyuta, I.O., Pometun, E.V., Hushpulian, D.M., Pometun, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 76.96 kDa
Atom Count: 5,210
Modeled Residue Count: 662
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-lactate dehydrogenase	A, B	341	Lacticaseibacillus rhamnosus	Mutation(s): 0 Gene Names: LRHM_0158
UniProt
Find proteins for A0A7S7JGB1 (Lacticaseibacillus rhamnosus (strain ATCC 53103 / LMG 18243 / GG)) Explore A0A7S7JGB1 Go to UniProtKB: A0A7S7JGB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7S7JGB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], E [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain H [auth B]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.324 (Depositor), 0.324 (DCC)
R-Value Work: 0.249 (Depositor), 0.249 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.326	α = 90
b = 80.25	β = 110.85
c = 70.225	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release