MolNFT v1 · #107525 · protein

Fragment bound to H.INFLUENZA NAD dependent DNA ligase

4UCU: “Fragment bound to H.INFLUENZA NAD dependent DNA ligase”. X-ray diffraction, 2 ligands (8HC, IWH), 4 pockets (best druggability 0.76). MolNFT v1 #107525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UCU
Type: protein
Length: 318 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA ligase
EC: 6.5.1.2
UniProt: P43813
Ligands: 8HC, IWH
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA ligase (EC 6.5.1.2)	protein	318	39% helix, 21% strand	P43813

Ligands and binding sites

8HC · 8-hydroxyquinoline-2-carboxylic acid · ligand · chains A
IWH · 1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide · ligand · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1074	0.76	0.78	70	8HC
2	224	0.49	0.75	35	empty
3	133	0.44	0.77	23	IWH
4	51	0.30	0.76	11	empty

Compared structures

4UCU · Fragment bound to H.influenza NAD dependent DNA ligase · the same entry in another collection · chain A against A, TM-score 1.00
P43813 · AlphaFold monomer V2.0 prediction for DNA ligase (P43813) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P43813
Elsewhere: RCSB PDB 4UCU · PDBe 4UCU · UniProt P43813

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