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Crystal structure of human tyrosyl-DNA phosphodiesterase (TDP1)

Analyse Crystal structure of human tyrosyl-DNA phosphodiesterase (TDP1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JY1
Type: protein
Length: 439 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-DNA phosphodiesterase
UniProt: Q9NUW8
Pockets: 4 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-DNA phosphodiesterase	protein	439	27% helix, 24% strand	Q9NUW8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	207	0.50	0.76	32	empty
2	171	0.48	0.77	22	empty
3	84	0.37	0.76	19	empty
4	55	0.34	0.78	20	empty

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

1JY1 · Crystal structure of human tyrosyl-DNA phosphodiesterase (TDP1) · the same entry in another collection · chain A against A, TM-score 1.00
Q9NUW8 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 1 (Q9NUW8) · a predicted model of the same protein · chain A 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 Q9NUW8
Elsewhere: RCSB PDB 1JY1 · PDBe 1JY1 · UniProt Q9NUW8

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