Research workbench
Structure of spastin hexamer (subunit a-E) in complex with substrate peptide
Analyse Structure of spastin hexamer (subunit a-E) in complex with substrate peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PEK
- Type
- protein
- Length
- 1,405 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spastin; Substrate peptide, tyr-glu-tyr-glu-tyr-glu-tyr-glu
- EC
- 5.6.1.1
- UniProt
- Q9UBP0
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spastin (EC 5.6.1.1) | protein | 283 | 47% helix, 8% strand | Q9UBP0 |
| B, C | Spastin (EC 5.6.1.1) | protein | 288 | 47% helix, 9% strand | Q9UBP0 |
| D | Spastin (EC 5.6.1.1) | protein | 293 | 49% helix, 9% strand | Q9UBP0 |
| E | Spastin (EC 5.6.1.1) | protein | 243 | 49% helix, 7% strand | Q9UBP0 |
| G | Substrate peptide, tyr-glu-tyr-glu-tyr-glu-tyr-glu | protein | 10 | 0% helix, 30% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- BEF · Beryllium trifluoride ion · ligand · 4 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.82 | 0.88 | 93 | empty |
| 2 | 940 | 0.80 | 0.82 | 82 | ADP, BEF, MG |
| 3 | 783 | 0.78 | 0.82 | 78 | ADP, BEF, MG |
| 4 | 628 | 0.77 | 0.83 | 62 | ADP, BEF, MG |
| 5 | 547 | 0.76 | 0.83 | 62 | ADP, BEF, MG |
Interfaces
10 interfaces between chains.
- C–D · 2467 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2431 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2422 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2344 Ų buried · 17 hydrogen bonds · protein-protein
- B–G · 373 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 Q9UBP0
- Elsewhere: RCSB PDB 6PEK · PDBe 6PEK · UniProt Q9UBP0
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