2DLD

D-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE

PDB DOI: https://doi.org/10.2210/pdb2DLD/pdb

Classification: OXIDOREDUCTASE (CHOH(D)-NAD+(A))
Organism(s): Lactobacillus helveticus
Mutation(s): No

Deposited: 1995-10-28 Released: 1996-03-14
Deposition Author(s): Dunn, C.R., Holbrook, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 ?
R-Value Free: 0.297
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Dehydrogenases Engineering to Correct Substrate Inhibition in a Commercial Dehydrogenase

Bernard, N., Delcour, J., Alvarez, A., Cortes, A., Willis, C., Holbrook, J.J.

To be published.

Macromolecule Content

Total Structure Weight: 77.17 kDa
Atom Count: 5,416
Modelled Residue Count: 674
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-LACTATE DEHYDROGENASE	A, B	337	Lactobacillus helveticus	Mutation(s): 0 EC: 1.1.1.28
UniProt
Find proteins for P30901 (Lactobacillus helveticus) Explore P30901 Go to UniProtKB: P30901
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30901
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
OXM Query on OXM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 ?
R-Value Free: 0.297
R-Value Observed: 0.195
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 86.2	α = 90
b = 62.1	β = 113.2
c = 77.4	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement
XENGEN	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1996-03-14

Deposition Author(s):

Dunn, C.R.

Holbrook, J.J.

Revision History (Full details and data files)

Version 1.0: 1996-03-14
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2013-11-06
Changes: Non-polymer description
Version 1.4: 2024-06-05
Changes: Data collection, Database references, Derived calculations, Other

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Help and Resources

2DLD

D-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE

Dehydrogenases Engineering to Correct Substrate Inhibition in a Commercial Dehydrogenase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)