Research workbench
Crystal structure of tubulin in complex with inhibitor D64
Analyse Crystal structure of tubulin in complex with inhibitor D64 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K9V
- Type
- protein
- Length
- 2,180 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.543
- Source
- Bos taurus; Gallus gallus; Rattus norvegicus
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, D3L, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.543 · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 427 | 45% helix, 19% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 44% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 421 | 49% helix, 20% strand | Q6B856 |
| E | Stathmin-4 | protein | 121 | 76% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 334 | 32% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- D3L · (5-methoxy-1H-indol-2-yl)-phenyl-methanone · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.84 | 0.86 | 118 | GTP, MG, D3L |
| 2 | 763 | 0.80 | 0.84 | 88 | GDP, MG |
| 3 | 165 | 0.79 | 0.95 | 37 | GTP, MG |
| 4 | 116 | 0.78 | 0.97 | 29 | D3L |
| 5 | 151 | 0.77 | 0.94 | 30 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1582 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1466 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 900 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 836 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6K9V · Crystal structure of tubulin in complex with inhibitor D64 · the same entry in another collection · chain F against F, TM-score 1.00
- P81947 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P81947) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P63043 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63043) · a predicted model of the same protein · chain E against A, TM-score 0.77
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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6K9V · PDBe 6K9V · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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