MolNFT v1 · #15100 · protein

Crystal structure of a human tyrosyl-DNA phosphodiesterase (TDP1)- vanadate complex

1MU9: “Crystal structure of a human tyrosyl-DNA phosphodiesterase (TDP1)- vanadate complex”. X-ray diffraction, 1 ligand (VO4), 6 pockets (best druggability 0.74). MolNFT v1 #15100 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1MU9
Type: protein
Length: 859 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-DNA phosphodiesterase
Ligands: VO4
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-DNA phosphodiesterase	protein	425	28% helix, 25% strand	—
B	Tyrosyl-DNA phosphodiesterase	protein	434	27% helix, 24% strand	—

Ligands and binding sites

VO4 · Vanadate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

6 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	1155	0.74	0.77	115	empty
2	270	0.55	0.77	32	VO4, GOL
3	251	0.52	0.76	34	VO4, GOL
4	82	0.41	0.79	20	empty
5	73	0.37	0.77	20	empty

Interfaces

1 interface between chains.

A–B · 632 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1MU9 · Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex · 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
Elsewhere: RCSB PDB 1MU9 · PDBe 1MU9

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