5KVV | pdb_00005kvv

Structure of Malate Dehydrogenase in complex with NADH from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb5KVV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-15 Released: 2016-09-14 
• Deposition Author(s): Cheng, Y.S., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure of Malate Dehydrogenase in complex with NADH from Mycobacterium tuberculosis

Cheng, Y.S., Sacchettini, J.C.

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: 72.13 kDa 
• Atom Count: 5,276 
• Modeled Residue Count: 653 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	335	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: mdh, Rv1240, MTV006.12 EC: 1.1.1.37
UniProt
Find proteins for P9WK13 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK13  Go to UniProtKB:  P9WK13

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	C [auth A], F [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.206	α = 90
b = 78.169	β = 90
c = 154.402	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Cheng, Y.S., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references, Derived calculations
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description