4I1I | pdb_00004i1i

Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb4I1I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leishmania major strain Friedlin
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-21 Released: 2012-12-19 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin in complex with NAD

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Edwards, T.E., Myler, P.

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)

Macromolecule Content 

• Total Structure Weight: 74.22 kDa 
• Atom Count: 5,343 
• Modeled Residue Count: 633 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	345	Leishmania major strain Friedlin	Mutation(s): 0  Gene Names: cMDH, LMJF_28_2860 EC: 1.1.1.37
UniProt
Find proteins for Q4Q7X6 (Leishmania major) Explore Q4Q7X6  Go to UniProtKB:  Q4Q7X6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4	D [auth A], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34I1I

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.82	α = 90
b = 65.13	β = 110.67
c = 77.49	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-10-22
  Changes: Database references, Structure summary