5YTA | pdb_00005yta

Pig Heart Lactate Dehydrogenase in complex with NADH and Oxamate

• PDB DOI: https://doi.org/10.2210/pdb5YTA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2017-11-17 Released: 2018-11-21 
• Deposition Author(s): Ho, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

pig heart lactate dehydrogenase in complex with NADH and oxamate

Ho, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 74.32 kDa 
• Atom Count: 5,403 
• Modeled Residue Count: 664 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase B chain	A, B	332	Sus scrofa	Mutation(s): 0  EC: 1.1.1.27
UniProt
Find proteins for P00336 (Sus scrofa) Explore P00336  Go to UniProtKB:  P00336

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
OXM	D [auth A], F [auth B]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OXM	BindingDB:  5YTA	Ki: 9.44e+4 (nM) from 1 assay(s)
		IC50: min: 3.38e+4, max: 1.23e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.788	α = 90
b = 130.788	β = 90
c = 111.909	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Ho, M.C.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references