Research workbench

Putative ATP-dependent DNA ligase from aquifex aeolicus.

Analyse Putative ATP-dependent DNA ligase from aquifex aeolicus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QWU
Type: protein
Length: 730 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA ligase
UniProt: O67191
Ligands: ADN, CA
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA ligase	protein	366	38% helix, 29% strand	O67191
B	DNA ligase	protein	364	38% helix, 29% strand	O67191

Ligands and binding sites

ADN · Adenosine · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

10 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	942	0.74	0.78	57	ADN
2	868	0.72	0.77	56	ADN
3	75	0.48	0.83	16	empty
4	121	0.48	0.79	24	empty
5	53	0.36	0.79	12	empty

Interfaces

1 interface between chains.

A–B · 2362 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3QWU · Putative ATP-dependent DNA ligase from Aquifex aeolicus. · the same entry in another collection · chain A against A, TM-score 1.00

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 O67191
Elsewhere: RCSB PDB 3QWU · PDBe 3QWU · UniProt O67191

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.