MolNFT v1 · #128621 · protein + DNA

Crystal structure of the complex of TDP1 with duplex DNA

5NWA · Tyrosyl-DNA phosphodiesterase 1: “Crystal structure of the complex of TDP1 with duplex DNA”. X-ray diffraction, 9 pockets (best druggability 0.77). MolNFT v1 #128621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NWA
Type: protein + DNA
Length: 883 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-DNA phosphodiesterase 1; DNA (5'-D(P*AP*AP*TP*GP*CP*GP*CP*AP*TP*TP*A)-3')
EC: 3.1.4.-
UniProt: Q9NUW8
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-)	protein	441	27% helix, 23% strand	Q9NUW8
C	DNA (5'-D(PAPAPTPGPCPGPCPAPTPTP*A)-3')	dna	10	—	—
B	Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-)	protein	432	27% helix, 25% strand	Q9NUW8

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1180	0.77	0.79	117	empty
2	193	0.51	0.77	23	empty
3	220	0.50	0.75	31	empty
4	122	0.39	0.75	20	empty
5	70	0.38	0.79	13	empty

Interfaces

2 interfaces between chains.

A–C · 606 Å² buried · 9 hydrogen bonds · protein-nucleic
A–B · 602 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5NWA · Crystal structure of the complex of Tdp1 with duplex DNA · 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 0.99

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 5NWA · PDBe 5NWA · UniProt Q9NUW8

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