Research workbench
Structure of SPAC806.04C protein from fission yeast covalently bound to BEF3
Analyse Structure of SPAC806.04C protein from fission yeast covalently bound to BEF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U1V
- Type
- protein
- Length
- 872 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Damage-control phosphatase SPAC806.04C
- EC
- 3.1.3.-
- UniProt
- Q9UT55
- Ligands
- NI, K, PO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Damage-control phosphatase SPAC806.04C (EC 3.1.3.-) | protein | 438 | 56% helix, 10% strand | Q9UT55 |
| B | Damage-control phosphatase SPAC806.04C (EC 3.1.3.-) | protein | 434 | 54% helix, 11% strand | Q9UT55 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B
- K · Potassium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.73 | 0.85 | 37 | empty |
| 2 | 604 | 0.72 | 0.79 | 72 | empty |
| 3 | 292 | 0.59 | 0.78 | 46 | empty |
| 4 | 67 | 0.42 | 0.81 | 20 | empty |
| 5 | 59 | 0.38 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7U1V · Structure of SPAC806.04c protein from fission yeast covalently bound to BeF3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UT55 · AlphaFold monomer V2.0 prediction for damage-control phosphatase SPAC806.04C (Q9UT55) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9UT55
- Elsewhere: RCSB PDB 7U1V · PDBe 7U1V · UniProt Q9UT55
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