Research workbench
Crystal structure of the binding domain of srebp from fission yeast
Analyse Crystal structure of the binding domain of srebp 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
- 5GPD
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterol regulatory element-binding protein 1
- UniProt
- Q9UUD1
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterol regulatory element-binding protein 1 | protein | 207 | 68% helix, 1% strand | Q9UUD1 |
| B | Sterol regulatory element-binding protein 1 | protein | 177 | 71% helix, 1% strand | Q9UUD1 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.86 | 0.86 | 68 | empty |
| 2 | 230 | 0.74 | 0.88 | 37 | empty |
| 3 | 83 | 0.46 | 0.81 | 19 | empty |
| 4 | 64 | 0.38 | 0.79 | 13 | empty |
| 5 | 62 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1172 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5GPD · Crystal structure of the binding domain of SREBP from fission yeast · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UUD1 · AlphaFold monomer V2.0 prediction for sterol regulatory element- binding protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9UUD1
- Elsewhere: RCSB PDB 5GPD · PDBe 5GPD · UniProt Q9UUD1
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