Research workbench
Tubulin-darpin complex
Analyse Tubulin-darpin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EYP
- Type
- protein
- Length
- 983 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Designed ankyrin repeat protein (darpin)
- UniProt
- D0VWZ0, D0VWY9
- Ligands
- GTP, GDP, LOC, MG, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 428 | 46% helix, 17% strand | D0VWZ0 |
| B | Tubulin beta chain | protein | 425 | 50% helix, 20% strand | D0VWY9 |
| F | Designed ankyrin repeat protein (darpin) | protein | 130 | 53% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- LOC · N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.83 | 0.84 | 106 | GTP, MG, SO4, GOL, LOC |
| 2 | 148 | 0.64 | 0.87 | 35 | GDP |
| 3 | 172 | 0.57 | 0.81 | 32 | empty |
| 4 | 64 | 0.51 | 0.85 | 17 | GOL |
| 5 | 63 | 0.50 | 0.86 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1451 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 629 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5EYP · Tubulin-darpin complex · 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 D0VWZ0
- Every structure of UniProt D0VWY9
- Elsewhere: RCSB PDB 5EYP · PDBe 5EYP · UniProt D0VWZ0 · UniProt D0VWY9
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