3PQD

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+

PDB DOI: https://doi.org/10.2210/pdb3PQD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-11-26 Released: 2012-01-18
Deposition Author(s): Zhang, Y., Garavito, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.269
R-Value Work: 0.214
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+

zhang, Y., Garavito, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 287.39 kDa
Atom Count: 19,005
Modelled Residue Count: 2,449
Deposited Residue Count: 2,608
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	326	Bacillus subtilis	Mutation(s): 0 Gene Names: ldh, lctE, BSU03050 EC: 1.1.1.27
UniProt
Find proteins for P13714 (Bacillus subtilis (strain 168)) Explore P13714 Go to UniProtKB: P13714
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13714
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D]	J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain L [auth F] SDF format, chain I [auth C] SDF format, chain M [auth G] MOL2 format, chain K [auth D] MOL2 format, chain L [auth F] MOL2 format, chain I [auth C] MOL2 format, chain M [auth G]	I [auth C], K [auth D], L [auth F], M [auth G]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Focus chain L [auth F] Focus chain M [auth G] Interactions & Density Focus chain I [auth C] Focus chain K [auth D] Focus chain L [auth F] Focus chain M [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.269
R-Value Work: 0.214
R-Value Observed: 0.215
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.041	α = 90
b = 171.041	β = 90
c = 96.272	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-18

Deposition Author(s):

Zhang, Y.

Garavito, R.M.

Revision History (Full details and data files)

Version 1.0: 2012-01-18
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Structure summary

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3PQD

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+

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)