MolNFT v1 · #58661 · protein

Structural basis for inhbition of NAD-dependent ligase

3BA9 · DNA ligase: “Structural basis for inhbition of NAD-dependent ligase”. X-ray diffraction, 3 ligands (NMN, 3B9, SO4), 4 pockets (best druggability 0.71). MolNFT v1 #58661 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BA9
Type: protein
Length: 313 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, 3B9, SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA ligase (EC 6.5.1.2)	protein	313	42% helix, 23% strand	Q837V6

Ligands and binding sites

NMN · Beta-nicotinamide ribose monophosphate · ligand · chains A
3B9 · N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide · ligand · chains A
SO4 · Sulfate ion · ion · 4 copies · chains A
GOL · Glycerol · additive · 3 copies · 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	413	0.71	0.82	46	SO4, 3B9, GOL
2	185	0.55	0.80	26	empty
3	71	0.36	0.77	23	empty
4	57	0.35	0.78	14	empty

Compared structures

3BA9 · Structural Basis for Inhbition of NAD-Dependent 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 3BA9 · PDBe 3BA9 · UniProt Q837V6

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