MolNFT v1 · #118772 · protein
Structure of a separase in complex with a pamk peptide containing a phospho-serine
5FC2 · Pamk, peptide containing a phospho-serine: “Structure of a separase in complex with a pamk peptide containing a phospho-serine”. X-ray diffraction, 1 ligand (6L3), 5 pockets (best druggability 0.58). MolNFT v1 #118772 on GenesisL1…
- PDB
- 5FC2
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pamk, peptide containing a phospho-serine; Separase
- UniProt
- G0SHM3
- Ligands
- 6L3
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pamk, peptide containing a phospho-serine | protein | 8 | 0% helix, 13% strand | — |
| B | Separase | protein | 482 | 48% helix, 14% strand | G0SHM3 |
Ligands and binding sites
- 6L3 · Methyl 2,4,6-trimethylbenzoate · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 107 | 0.58 | 0.85 | 25 | empty |
| 2 | 296 | 0.51 | 0.74 | 39 | empty |
| 3 | 114 | 0.42 | 0.77 | 17 | empty |
| 4 | 80 | 0.36 | 0.76 | 16 | empty |
| 5 | 58 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5FC2 · Structure of a separase in complex with a pAMK peptide containing a phospho-serine · the same entry in another collection · chain A against A, TM-score 1.00
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 G0SHM3
- Elsewhere: RCSB PDB 5FC2 · PDBe 5FC2 · UniProt G0SHM3
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