7K72

Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD

Delker, S.L.Abendroth, J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase AA, B, C, D336Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ligAligRv3014cMTV012.28c
EC: 6.5.1.2
UniProt
Find proteins for P9WNV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNV1 
Go to UniProtKB:  P9WNV1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], P [auth C], T [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], O [auth B], S [auth C], X [auth D](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A], M [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , K [auth B] , L [auth B] , Q [auth C] , R [auth C] , U [auth D] , V [auth D] , 
F [auth A],  G [auth A],  K [auth B],  L [auth B],  Q [auth C],  R [auth C],  U [auth D],  V [auth D],  W [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.94α = 96.22
b = 63.81β = 89.55
c = 120.73γ = 111.97
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release