3BA9

Structural Basis for Inhbition of NAD-Dependent Ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Inhbition of NAD-Dependent Ligase

Pinko, C.Borchardt, A.Nikulin, V.Su, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase332Enterococcus faecalisMutation(s): 0 
Gene Names: ligA
EC: 6.5.1.2
UniProt
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q837V6 
Go to UniProtKB:  Q837V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ837V6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3B9
Query on 3B9

Download Ideal Coordinates CCD File 
G [auth A]N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide
C24 H24 N6 O2
FDJWFDQRPKKBFA-UHFFFAOYSA-N
NMN
Query on NMN

Download Ideal Coordinates CCD File 
F [auth A]BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.248α = 90
b = 86.277β = 101.11
c = 57.143γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2008-11-11 
  • Deposition Author(s): Pinko, C.

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations