4LMP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine dehydrogenase371Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: aldRVBD_2780
EC: 1.4.1.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6MD
Query on 6MD

Download Ideal Coordinates CCD File 
B [auth A]N-methyladenosine
C11 H15 N5 O4
VQAYFKKCNSOZKM-IOSLPCCCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.73α = 90
b = 89.73β = 90
c = 290.401γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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