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Crystal structure of truncated USP1-UAF1

Analyse Crystal structure of truncated USP1-UAF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AY0
Type: protein
Length: 1,610 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Wd repeat-containing protein 48; Ubiquitin carboxyl-terminal hydrolase 1
EC: 3.4.19.12
UniProt: Q8TAF3
Ligands: ZN
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Wd repeat-containing protein 48	protein	512	10% helix, 43% strand	Q8TAF3
B	Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.4.19.12)	protein	302	29% helix, 29% strand	—
C	Wd repeat-containing protein 48	protein	511	10% helix, 42% strand	Q8TAF3
D	Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.4.19.12)	protein	285	28% helix, 31% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.80	0.86	61	empty
2	743	0.80	0.84	60	empty
3	68	0.72	0.96	15	empty
4	427	0.69	0.81	48	empty
5	401	0.69	0.81	47	empty

Interfaces

3 interfaces between chains.

C–D · 848 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 846 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 279 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7AY0 · Crystal structure of truncated USP1-UAF1 · the same entry in another collection · chain A against A, TM-score 1.00
Q8TAF3 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 48 (Q8TAF3) · a predicted model of the same protein · chain C 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 Q8TAF3
Elsewhere: RCSB PDB 7AY0 · PDBe 7AY0 · UniProt Q8TAF3

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