4PLH

Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 4PLH

Classification: OXIDOREDUCTASE

Total Structure Weight: 146321.19

Macromolecule Entities
Molecule Chains Length Organism Details
malate dehydrogenase A, B, C, D 326 Apicomplexa Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAI
Query on NAI

A, B, C, D 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH (Synonym)
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXM
Query on OXM

A, B, C, D OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.181
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 89.42 α = 90.00
b = 104.57 β = 90.00
c = 142.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-05-16
  • Released Date: 2014-07-02
  • Deposition author(s): Boucher, J.I., Jacobowitz, J.R., Beckett, B.C., Classen, S., Theobald, D.L.

Revision History

  • Version 1_0: 2014-07-02

    Type: Initial release

  • Version 1_1: 2014-07-09

    Type: Structure summary

  • Version 1_2: 2014-07-16

    Type: Database references

  • Version 1_3: 2014-09-24

    Type: Structure summary

  • Version 1_4: 2014-10-01

    Type: Database references

  • Version 1_5: 2017-09-27

    Type: Author supporting evidence, Derived calculations, Other, Source and taxonomy