1LDN

STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1LDN/pdb

Classification: OXIDOREDUCTASE(CHOH(D)-NAD(A))
Organism(s): Geobacillus stearothermophilus
Mutation(s): No

Deposited: 1991-11-19 Released: 1994-01-31
Deposition Author(s): Wigley, D.B., Gamblin, S.J., Turkenburg, J.P., Dodson, E.J., Piontek, K., Muirhead, H., Holbrook, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 285.34 kDa
Atom Count: 20,716
Modelled Residue Count: 2,528
Deposited Residue Count: 2,528
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LACTATE DEHYDROGENASE	A, B, C, D, E A, B, C, D, E, F, G, H	316	Geobacillus stearothermophilus	Mutation(s): 0 EC: 1.1.1.27
UniProt
Find proteins for P00344 (Geobacillus stearothermophilus) Explore P00344 Go to UniProtKB: P00344
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00344
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain Z [auth G] SDF format, chain BA [auth H] SDF format, chain P [auth C] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain P [auth C] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F]	BA [auth H] K [auth A] N [auth B] P [auth C] R [auth D] BA [auth H], K [auth A], N [auth B], P [auth C], R [auth D], U [auth E], X [auth F], Z [auth G]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Focus chain Z [auth G]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain S [auth E] SDF format, chain I [auth A] SDF format, chain V [auth F] MOL2 format, chain L [auth B] MOL2 format, chain S [auth E] MOL2 format, chain I [auth A] MOL2 format, chain V [auth F]	I [auth A], L [auth B], S [auth E], V [auth F]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain S [auth E] Focus chain V [auth F]
OXM Query on OXM Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain AA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Y [auth G] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain AA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Y [auth G]	AA [auth H] J [auth A] M [auth B] O [auth C] Q [auth D] AA [auth H], J [auth A], M [auth B], O [auth C], Q [auth D], T [auth E], W [auth F], Y [auth G]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.9	α = 90
b = 118.2	β = 96.07
c = 135.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1994-01-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1994-01-31
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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Structure summary