MolNFT v1 · #127524 · protein
Cryo-EM structure of a separase-securin complex from caenorhabditis elegans at 3.8 a resolution
5MZ6: “Cryo-EM structure of a separase-securin complex from caenorhabditis elegans at 3.8 a resolution”. Electron microscopy, 14 pockets (best druggability 0.71). MolNFT v1 #127524 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5MZ6
- Type
- protein
- Length
- 1,092 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Separase; Interactor of fizzy protein
- UniProt
- G5ED39, Q18235
- Pockets
- 14 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Separase | protein | 1018 | 58% helix, 6% strand | G5ED39 |
| B | Interactor of fizzy protein | protein | 74 | 8% helix, 3% strand | Q18235 |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.71 | 0.80 | 72 | empty |
| 2 | 104 | 0.70 | 0.93 | 21 | empty |
| 3 | 388 | 0.67 | 0.80 | 51 | empty |
| 4 | 231 | 0.59 | 0.80 | 33 | empty |
| 5 | 191 | 0.58 | 0.81 | 28 | empty |
Interfaces
1 interface between chains.
- 1–B · 2829 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5MZ6 · Cryo-EM structure of a Separase-Securin complex from Caenorhabditis elegans at 3.8 A… · the same entry in another collection · chain 1 against 1, TM-score 1.00
- G5ED39 · AlphaFold monomer V2.0 prediction for separin homolog sep-1 (G5ED39) · a predicted model of the same protein · chain 1 against A, TM-score 0.98
- Q18235 · AlphaFold monomer V2.0 prediction for securin-like protein (Q18235) · a predicted model of the same protein · chain B against A, TM-score 0.27
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 G5ED39
- Every structure of UniProt Q18235
- Elsewhere: RCSB PDB 5MZ6 · PDBe 5MZ6 · UniProt G5ED39 · UniProt Q18235
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