3BAB

Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase

Structural Biology Knowledgebase: 3BAB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BAB

Classification: LIGASE

Total Structure Weight: 39252.13

Macromolecule Entities
Molecule Chains Length Organism Details
DNA ligase A 332 Enterococcus faecalis EC#: 6.5.1.2 IUBMB
Fragment: Adenylation Domain
Gene Name(s): ligA EF_0722

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

A 7-amino-2-tert-butyl-4-(4-pyrimidin-2-ylpiperazin- 1-yl)pyrido[2,3-d]pyrimidine-6-carboxamide
C20 H25 N9 O
CKLCIJCZOIDJQU-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
NMN
Query on NMN

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

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.197
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 90.57 α = 90.00
b = 86.73 β = 100.99
c = 56.86 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