Research workbench
Structure, thermodynamics, and kinetics of plinabulin binding to two tubulin isotypes
Analyse Structure, thermodynamics, and kinetics of plinabulin binding to two tubulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S8L
- Type
- protein
- Length
- 999 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain; Designed ankyrin repeat protein (darpin) D1
- UniProt
- P68363, Q13509
- Ligands
- GTP, PN6, GDP, MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 424 | 46% helix, 17% strand | P68363 |
| B | Tubulin beta-3 chain | protein | 420 | 50% helix, 18% strand | Q13509 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 54% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- PN6 · (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione · ligand · chains B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.81 | 0.84 | 96 | GTP, MG, PN6 |
| 2 | 241 | 0.61 | 0.81 | 30 | empty |
| 3 | 191 | 0.57 | 0.81 | 28 | GDP, MG |
| 4 | 56 | 0.56 | 0.90 | 18 | empty |
| 5 | 139 | 0.54 | 0.81 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1390 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 916 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6S8L · Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes · the same entry in another collection · chain A against A, TM-score 1.00
- Q13509 · AlphaFold monomer V2.0 prediction for tubulin beta-3 chain (Q13509) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P68363 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P68363) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P68363
- Every structure of UniProt Q13509
- Elsewhere: RCSB PDB 6S8L · PDBe 6S8L · UniProt P68363 · UniProt Q13509
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