MolNFT v1 · #159757 · protein
Spastin hexamer in complex with substrate
6P07: “Spastin hexamer in complex with substrate”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #159757 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P07
- Type
- protein
- Length
- 1,795 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spastin; Polyglutamate peptide
- EC
- 5.6.1.1
- UniProt
- A0A126GV13
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spastin (EC 5.6.1.1) | protein | 270 | 50% helix, 7% strand | A0A126GV13 |
| B, D, E | Spastin (EC 5.6.1.1) | protein | 303 | 47% helix, 9% strand | A0A126GV13 |
| C | Spastin (EC 5.6.1.1) | protein | 301 | 41% helix, 9% strand | A0A126GV13 |
| F | Spastin (EC 5.6.1.1) | protein | 300 | 42% helix, 8% strand | A0A126GV13 |
| G | Polyglutamate peptide | protein | 15 | 0% helix, 27% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · chains F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.81 | 0.83 | 74 | ATP, MG |
| 2 | 1172 | 0.81 | 0.82 | 103 | ATP, MG |
| 3 | 1063 | 0.80 | 0.82 | 121 | empty |
| 4 | 872 | 0.80 | 0.82 | 78 | ATP, MG |
| 5 | 1023 | 0.79 | 0.81 | 95 | ATP, MG |
Interfaces
14 interfaces between chains.
- C–D · 2690 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 2615 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2610 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2574 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2569 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6P07 · Spastin hexamer in complex with substrate · 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 A0A126GV13
- Elsewhere: RCSB PDB 6P07 · PDBe 6P07 · UniProt A0A126GV13
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