Research workbench
Drosophila GTP-tubulin Y222F mutant
Analyse Drosophila GTP-tubulin Y222F mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TIU
- Type
- protein
- Length
- 1,846 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1 chain; Tubulin beta-1 chain; Stathmin-4
- UniProt
- P06603, Q24560, P63043
- Ligands
- GTP, GDP, MG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1 chain | protein | 432 | 46% helix, 18% strand | P06603 |
| B | Tubulin beta-1 chain | protein | 428 | 49% helix, 19% strand | Q24560 |
| C | Tubulin alpha-1 chain | protein | 432 | 45% helix, 18% strand | P06603 |
| D | Tubulin beta-1 chain | protein | 427 | 49% helix, 19% strand | Q24560 |
| E | Stathmin-4 | protein | 127 | 74% helix, 13% strand | P63043 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.82 | 0.84 | 88 | GTP, MG, GDP |
| 2 | 1115 | 0.80 | 0.81 | 113 | GTP, MG |
| 3 | 418 | 0.75 | 0.85 | 58 | GTP, MG |
| 4 | 534 | 0.69 | 0.79 | 50 | empty |
| 5 | 400 | 0.69 | 0.81 | 35 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1705 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1427 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1384 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1356 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 861 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TIU · Drosophila GTP-tubulin Y222F mutant · the same entry in another collection · chain E against E, TM-score 1.00
- Q24560 · AlphaFold monomer V2.0 prediction for tubulin beta-1 chain (Q24560) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P06603 · AlphaFold monomer V2.0 prediction for tubulin alpha-1 chain (P06603) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P06603
- Every structure of UniProt Q24560
- Every structure of UniProt P63043
- Elsewhere: RCSB PDB 6TIU · PDBe 6TIU · UniProt P06603 · UniProt Q24560 · UniProt P63043
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