5ZJD

Lactate dehydrogenase with NADH and MLA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.394 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Machilin A Inhibits Tumor Growth and Macrophage M2 Polarization Through the Reduction of Lactic Acid

Chung, T.-W.Kim, E.-Y.Han, C.W.Park, S.Y.Jeong, M.S.Yoon, D.Choi, H.-J.Jin, L.Park, M.-J.Kwon, Y.J.Lee, H.Kim, K.-J.Park, K.H.Kim, S.Jang, S.B.Ha, K.-T.

(2019) Cancers (Basel) 11: 963-963


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-lactate dehydrogenase A chain
A, B, C, D, E, F, G, H
337Homo sapiensMutation(s): 0 
Gene Names: LDHA
EC: 1.1.1.27
Find proteins for P00338 (Homo sapiens)
Go to Gene View: LDHA
Go to UniProtKB:  P00338
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.394 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.007α = 90.00
b = 265.691β = 103.17
c = 88.006γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-03-20 
  • Released Date: 2019-07-24 
  • Deposition Author(s): Jang, S.B., Han, C.W.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2015R1D1A1A01059594

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release