Research workbench
Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg
Analyse Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AY2
- Type
- protein
- Length
- 1,695 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 48; Ubiquitin carboxyl-terminal hydrolase 1; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q8TAF3, P0CG47
- Ligands
- AYE, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 48 | protein | 514 | 9% helix, 43% strand | Q8TAF3 |
| B | Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.4.19.12) | protein | 337 | 35% helix, 29% strand | — |
| C | Polyubiquitin-B | protein | 75 | 24% helix, 32% strand | P0CG47 |
| D | Wd repeat-containing protein 48 | protein | 508 | 9% helix, 43% strand | Q8TAF3 |
| E | Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.4.19.12) | protein | 203 | 33% helix, 33% strand | — |
| F | Polyubiquitin-B | protein | 58 | 24% helix, 24% strand | P0CG47 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.82 | 0.86 | 64 | empty |
| 2 | 742 | 0.81 | 0.84 | 65 | empty |
| 3 | 726 | 0.74 | 0.80 | 67 | empty |
| 4 | 823 | 0.70 | 0.76 | 63 | empty |
| 5 | 215 | 0.68 | 0.86 | 28 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1845 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 1198 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1035 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 852 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7AY2 · Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg · the same entry in another collection · chain F against F, 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 D 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
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 7AY2 · PDBe 7AY2 · UniProt Q8TAF3 · UniProt P0CG47
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