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Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I. monoclinic form

Analyse Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CY9
Type: protein
Length: 488 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: P06612
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA topoisomerase I (EC 5.99.1.2)	protein	245	32% helix, 31% strand	P06612
B	DNA topoisomerase I (EC 5.99.1.2)	protein	243	33% helix, 31% strand	P06612

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	190	0.52	0.78	25	empty

Interfaces

1 interface between chains.

A–B · 376 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1CY9 · Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I. monoclinic form · the same entry in another collection · chain A against A, TM-score 1.00
P06612 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P06612) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P06612
Elsewhere: RCSB PDB 1CY9 · PDBe 1CY9 · UniProt P06612

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