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Structural basis for the inhibition of bacterial NAD+ dependent DNA ligase

Analyse Structural basis for the inhibition of bacterial NAD+ dependent DNA ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BAB
Type: protein
Length: 312 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA ligase
EC: 6.5.1.2
UniProt: Q837V6
Ligands: NMN, 3BD, SO4
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA ligase (EC 6.5.1.2)	protein	312	41% helix, 23% strand	Q837V6

Ligands and binding sites

NMN · Beta-nicotinamide ribose monophosphate · ligand · chains A
3BD · 7-amino-2-tert-butyl-4-(4-pyrimidin-2-ylpiperazin-1-yl)pyrido[2,3-d]pyrimidine-6-carboxamide · ligand · chains A
SO4 · Sulfate ion · ion · 4 copies · chains A
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	463	0.72	0.82	47	3BD
2	202	0.57	0.80	33	GOL
3	63	0.40	0.80	17	NMN
4	83	0.34	0.75	27	empty

Compared structures

3BAB · Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase · the same entry in another collection · chain A against A, TM-score 1.00
Q837V6 · AlphaFold monomer V2.0 prediction for DNA ligase (Q837V6) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q837V6
Elsewhere: RCSB PDB 3BAB · PDBe 3BAB · UniProt Q837V6

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