4LMP | pdb_00004lmp

Mycobacterium tuberculosis L-alanine dehydrogenase x-ray structure in complex with N6-methyl adenosine

• PDB DOI: https://doi.org/10.2210/pdb4LMP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-10 Released: 2013-11-06 
• Deposition Author(s): Kim, H.-B., Hung, L.-W., Goulding, C.W., Terwilliger, T.C., Kim, C.-Y., Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Drug target analysis by dye-ligand affinity chromatography

Kim, H.-B., Hung, L.-W., Goulding, C.W., Terwilliger, T.C., Kim, C.-Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.69 kDa 
• Atom Count: 3,011 
• Modeled Residue Count: 371 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine dehydrogenase	A	371	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ald, RVBD_2780 EC: 1.4.1.1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6MD	B [auth A]	N-methyladenosine C11 H15 N5 O4 VQAYFKKCNSOZKM-IOSLPCCCSA-N
SO4	G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.73	α = 90
b = 89.73	β = 90
c = 290.401	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Kim, H.-B., Hung, L.-W., Goulding, C.W., Terwilliger, T.C., Kim, C.-Y., Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description