Research workbench
GTPase domain of septin 9 in complex with GTP-gamma-S
Analyse GTPase domain of septin 9 in complex with GTP-gamma-S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CYP
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Septin-9
- UniProt
- Q9UHD8
- Ligands
- GSP, MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Septin-9 | protein | 248 | 43% helix, 18% strand | Q9UHD8 |
| B | Septin-9 | protein | 227 | 47% helix, 18% strand | Q9UHD8 |
| C | Septin-9 | protein | 238 | 45% helix, 18% strand | Q9UHD8 |
| D | Septin-9 | protein | 227 | 48% helix, 19% strand | Q9UHD8 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 4 copies · chains A, B, C, D
- 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.81 | 0.87 | 71 | GSP, MG |
| 2 | 455 | 0.78 | 0.86 | 63 | GSP, MG |
| 3 | 283 | 0.65 | 0.81 | 44 | GSP, MG |
| 4 | 300 | 0.64 | 0.81 | 40 | GSP, MG |
| 5 | 73 | 0.39 | 0.78 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1148 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1034 Ų buried · 14 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 Q9UHD8
- Elsewhere: RCSB PDB 5CYP · PDBe 5CYP · UniProt Q9UHD8
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