2FN7 | pdb_00002fn7

Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (lactic acid) and cofactor (b-nicotinamide adenine dinucleotide)

• PDB DOI: https://doi.org/10.2210/pdb2FN7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cryptosporidium parvum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-01-10 Released: 2007-01-23 
• Deposition Author(s): Senkovich, O.A., Chattopadhyay, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 

Starting Model: experimental

Literature

Structure of cryptosporidium parvum lactate dehydrogenase in complex with substrates and cofactors

Senkovich, O.A., Chattopadhyay, D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.46 kDa 
• Atom Count: 4,965 
• Modeled Residue Count: 634 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactate Dehydrogenase	A, B	321	Cryptosporidium parvum	Mutation(s): 0  Gene Names: LDH1 EC: 1.1.1.27
UniProt
Find proteins for Q5CYZ2 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CYZ2  Go to UniProtKB:  Q5CYZ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	E [auth A], F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
LAC	D [auth A]	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.47	α = 90
b = 95.47	β = 90
c = 186.04	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Senkovich, O.A., Chattopadhyay, D.

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection