Research workbench

Human topoisomerase iiib topo domain

Analyse Human topoisomerase iiib topo domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GVC
Type: protein
Length: 1,215 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA topoisomerase 3-beta-1
EC: 5.99.1.2
UniProt: O95985
Ligands: MG
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA topoisomerase 3-beta-1 (EC 5.99.1.2)	protein	612	42% helix, 20% strand	O95985
B	DNA topoisomerase 3-beta-1 (EC 5.99.1.2)	protein	603	42% helix, 21% strand	O95985

Ligands and binding sites

MG · Magnesium ion · metal · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	813	0.77	0.81	92	MG
2	777	0.72	0.78	72	MG
3	144	0.58	0.83	24	empty
4	69	0.54	0.87	20	empty
5	151	0.43	0.75	29	empty

Interfaces

1 interface between chains.

A–B · 692 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5GVC · Human Topoisomerase IIIb topo domain · the same entry in another collection · chain A against A, TM-score 1.00
O95985 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 3-beta-1 (O95985) · 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 O95985
Elsewhere: RCSB PDB 5GVC · PDBe 5GVC · UniProt O95985

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