Research workbench

Wild-type uracil-DNA glycosylase bound to uracil-containing DNA

Analyse Wild-type uracil-DNA glycosylase bound to uracil-containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SSP
Type: protein + DNA
Length: 243 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*TP*GP*TP*(D1P)P*AP*TP*CP*TP*T)-3'; 5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3'…
EC: 3.2.2.3
UniProt: P13051
Ligands: ORP, URA
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(CPTPGPTP(D1P)PAPTPCPTPT)-3'	dna	9	—	—
B	5'-D(APAPAPGPAPTPAPAPCPAP*G)-3'	dna	11	—	—
E	Uracil-DNA glycosylase (EC 3.2.2.3)	protein	223	40% helix, 11% strand	P13051

Ligands and binding sites

ORP · 2-deoxy-5-phosphono-ribose · ligand · chains A, E
URA · Uracil · ligand · chains E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.68	0.94	30	ORP, URA
2	253	0.48	0.74	24	empty
3	121	0.41	0.76	17	empty
4	60	0.32	0.75	13	empty

Interfaces

3 interfaces between chains.

A–E · 503 Å² buried · 6 hydrogen bonds · protein-nucleic
A–B · 433 Å² buried · 41 hydrogen bonds · nucleic-nucleic
B–E · 213 Å² buried · 1 hydrogen bond · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1SSP · Wild-type uracil-DNA glycosylase bound to uracil-containing DNA · the same entry in another collection · chain A against A, TM-score 1.00
P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 P13051
Elsewhere: RCSB PDB 1SSP · PDBe 1SSP · UniProt P13051

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