Research workbench
GTP-tubulin in complex with a darpin
Analyse GTP-tubulin in complex with a darpin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DRX
- Type
- protein
- Length
- 2,018 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Designed ankyrin repeat protein (darpin) D1
- UniProt
- D0VWZ0, D0VWY9
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 431 | 44% helix, 18% strand | D0VWZ0 |
| B | Tubulin beta chain | protein | 424 | 49% helix, 18% strand | D0VWY9 |
| C | Tubulin alpha chain | protein | 421 | 46% helix, 18% strand | D0VWZ0 |
| D | Tubulin beta chain | protein | 431 | 48% helix, 19% strand | D0VWY9 |
| E | Designed ankyrin repeat protein (darpin) D1 | protein | 156 | 52% helix, 0% strand | — |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 52% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · 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
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.78 | 0.87 | 56 | GTP, MG |
| 2 | 445 | 0.77 | 0.86 | 55 | GTP, MG |
| 3 | 1105 | 0.74 | 0.77 | 83 | empty |
| 4 | 565 | 0.68 | 0.78 | 51 | empty |
| 5 | 545 | 0.68 | 0.78 | 47 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1381 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1367 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 970 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 930 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 338 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4DRX · GTP-Tubulin in complex with a DARPIN · 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 4DRX · PDBe 4DRX · UniProt D0VWZ0 · UniProt D0VWY9
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