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Crystal structure of topo-78, an N-terminal 78KDA fragment of topoisomerase V

Analyse Crystal structure of topo-78, an N-terminal 78KDA fragment of topoisomerase V in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GFJ
Type: protein
Length: 610 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Topoisomerase V
UniProt: F1SVL0
Ligands: ZN
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Topoisomerase V	protein	610	64% helix, 2% strand	F1SVL0

Ligands and binding sites

ZN · Zinc ion · metal · chains A
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

6 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	677	0.78	0.83	66	GOL
2	173	0.59	0.82	23	empty
3	210	0.54	0.78	31	empty
4	114	0.54	0.82	19	empty
5	75	0.31	0.74	20	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4GFJ · Crystal structure of Topo-78, an N-terminal 78kDa fragment of topoisomerase V · 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 F1SVL0
Elsewhere: RCSB PDB 4GFJ · PDBe 4GFJ · UniProt F1SVL0

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