Research workbench
Crystal structure of SFI1P/CDC31P complex
Analyse Crystal structure of SFI1P/CDC31P complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DOQ
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 31; SFI1P
- UniProt
- P06704, Q12369
- Ligands
- CA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 31 | protein | 146 | 60% helix, 4% strand | P06704 |
| B | Cell division control protein 31 | protein | 149 | 59% helix, 4% strand | P06704 |
| C | Cell division control protein 31 | protein | 130 | 57% helix, 3% strand | P06704 |
| D | SFI1P | protein | 83 | 87% helix, 0% strand | Q12369 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.70 | 0.81 | 29 | empty |
| 2 | 353 | 0.63 | 0.78 | 40 | empty |
| 3 | 212 | 0.59 | 0.80 | 26 | empty |
| 4 | 222 | 0.55 | 0.78 | 24 | empty |
| 5 | 249 | 0.54 | 0.77 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1575 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1189 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 921 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 302 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 294 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 2DOQ · crystal structure of Sfi1p/Cdc31p complex · the same entry in another collection · chain D against D, TM-score 1.00
- P06704 · AlphaFold monomer V2.0 prediction for cell division control protein 31 (P06704) · a predicted model of the same protein · chain C against A, TM-score 0.84
- Q12369 · AlphaFold monomer V2.0 prediction for protein SFI1 (Q12369) · a predicted model of the same protein · chain D against A, TM-score 0.83
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 P06704
- Every structure of UniProt Q12369
- Elsewhere: RCSB PDB 2DOQ · PDBe 2DOQ · UniProt P06704 · UniProt Q12369
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