3BA9

Structural Basis for Inhbition of NAD-Dependent Ligase

Structural Biology Knowledgebase: 3BA9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BA9

Classification: LIGASE

Total Structure Weight: 39457.30

Macromolecule Entities
Molecule Chains Length Organism Details
DNA ligase A 332 Enterococcus faecalis EC#: 6.5.1.2 IUBMB
Gene Name(s): ligA EF_0722
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3B9
Query on 3B9

A N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7- yl)-2-methylpropyl]-4-phenoxybenzamide
C24 H24 N6 O2
FDJWFDQRPKKBFA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NMN
Query on NMN

A BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
NICOTINAMIDE MONONUCLEOTIDE (Synonym)
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.184
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 90.25 α = 90.00
b = 86.28 β = 101.11
c = 57.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-07
  • Released Date: 2008-11-11
  • Deposition author(s): Pinko, C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update