Research workbench
Crystal structure of the WD40 domain of scap from fission yeast
Analyse Crystal structure of the WD40 domain of scap from fission yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YHC
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterol regulatory element-binding protein cleavage- activating protein
- UniProt
- O43043
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterol regulatory element-binding protein cleavage- activating protein | protein | 439 | 4% helix, 54% strand | O43043 |
| B | Sterol regulatory element-binding protein cleavage- activating protein | protein | 411 | 3% helix, 54% strand | O43043 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.75 | 0.77 | 70 | empty |
| 2 | 1080 | 0.74 | 0.77 | 78 | empty |
| 3 | 374 | 0.60 | 0.77 | 37 | empty |
| 4 | 275 | 0.53 | 0.76 | 36 | empty |
| 5 | 54 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 404 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4YHC · Crystal structure of the WD40 domain of SCAP from fission yeast · the same entry in another collection · chain A against A, TM-score 1.00
- O43043 · AlphaFold monomer V2.0 prediction for sterol regulatory element- binding protein… · 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 O43043
- Elsewhere: RCSB PDB 4YHC · PDBe 4YHC · UniProt O43043
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