3D4P | pdb_00003d4p

Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate

• PDB DOI: https://doi.org/10.2210/pdb3D4P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-14 Released: 2009-06-02 
• Deposition Author(s): Schramm, V.L., Almo, S.C., Gutierrez, J.A., Ho, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate

Schramm, V.L., Almo, S.C., Gutierrez, J.A., Ho, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.75 kDa 
• Atom Count: 5,216 
• Modeled Residue Count: 617 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase 1	A, B	317	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: ldh1, SACOL0222 EC: 1.1.1.27
UniProt
Find proteins for Q5HJD7 (Staphylococcus aureus (strain COL)) Explore Q5HJD7  Go to UniProtKB:  Q5HJD7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PYR	D [auth A], F [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.868	α = 90
b = 74.916	β = 128.9
c = 95.874	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Schramm, V.L., Almo, S.C., Gutierrez, J.A., Ho, M.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations