MolNFT v1 · #171294 · protein

DNA topoisomerase

6Z01 · DNA topoisomerase I: “DNA topoisomerase”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.77). MolNFT v1 #171294 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Z01
Type: protein
Length: 1,038 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA topoisomerase I
EC: 5.99.1.2
UniProt: E6NAV3
Ligands: CL
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA topoisomerase I (EC 5.99.1.2)	protein	521	50% helix, 12% strand	E6NAV3
B	DNA topoisomerase I (EC 5.99.1.2)	protein	517	49% helix, 13% strand	E6NAV3

Ligands and binding sites

CL · Chloride ion · ion · 12 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.77	0.80	70	empty
2	1107	0.72	0.75	94	CL
3	699	0.68	0.75	73	CL
4	71	0.46	0.82	21	empty
5	60	0.40	0.81	15	CL

Interfaces

1 interface between chains.

A–B · 796 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

6Z01 · DNA Topoisomerase · 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 E6NAV3
Elsewhere: RCSB PDB 6Z01 · PDBe 6Z01 · UniProt E6NAV3

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