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Ccdb, a topoisomerase poison from E. COLI

Analyse Ccdb, a topoisomerase poison from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VUB
Type: protein
Length: 394 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ccdb
UniProt: P62554
Ligands: CL
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ccdb	protein	95	26% helix, 34% strand	P62554
B, C	Ccdb	protein	101	25% helix, 38% strand	P62554
D	Ccdb	protein	97	26% helix, 35% strand	P62554

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.37	0.74	26	empty

Interfaces

2 interfaces between chains.

A–B · 1058 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1036 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1VUB · Ccdb, a topoisomerase poison from E. COLI · the same entry in another collection · chain D against D, TM-score 1.00
P62554 · AlphaFold monomer V2.0 prediction for toxin ccdb (P62554) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P62554
Elsewhere: RCSB PDB 1VUB · PDBe 1VUB · UniProt P62554

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