Research workbench
Tubulin: RB3 Stathmin-like domain complex
Analyse Tubulin: RB3 Stathmin-like domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HKB
- Type
- protein
- Length
- 1,818 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.65
- Source
- Ovis aries; Rattus norvegicus
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-4
- UniProt
- P63043
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 3.65 · 5 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 427 | 43% helix, 14% strand | — |
| B | Tubulin beta chain | protein | 420 | 45% helix, 15% strand | — |
| C | Tubulin alpha chain | protein | 428 | 42% helix, 14% strand | — |
| D | Tubulin beta chain | protein | 419 | 46% helix, 15% strand | — |
| E | Stathmin-4 | protein | 124 | 44% helix, 6% strand | P63043 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.83 | 0.84 | 120 | GDP |
| 2 | 964 | 0.78 | 0.80 | 101 | GTP, MG |
| 3 | 428 | 0.75 | 0.84 | 54 | GTP, MG |
| 4 | 504 | 0.73 | 0.82 | 53 | empty |
| 5 | 481 | 0.68 | 0.79 | 37 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1510 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1186 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1174 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 964 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 740 Ų buried · 4 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 P63043
- Elsewhere: RCSB PDB 3HKB · PDBe 3HKB · UniProt P63043
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