Research workbench
Drosophila GDP-tubulin Y222F mutant
Analyse Drosophila GDP-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
- 6TIZ
- Type
- protein
- Length
- 1,844 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
- 17 · 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 | 430 | 46% helix, 18% strand | P06603 |
| B | Tubulin beta-1 chain | protein | 428 | 50% helix, 19% strand | Q24560 |
| C | Tubulin alpha-1 chain | protein | 430 | 45% helix, 18% strand | P06603 |
| D | Tubulin beta-1 chain | protein | 427 | 49% helix, 20% strand | Q24560 |
| E | Stathmin-4 | protein | 129 | 73% helix, 13% 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, B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 2 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.82 | 0.85 | 91 | GDP |
| 2 | 1024 | 0.80 | 0.82 | 104 | GTP, MG, GOL |
| 3 | 923 | 0.79 | 0.81 | 100 | GTP, MG |
| 4 | 533 | 0.70 | 0.79 | 49 | GOL |
| 5 | 415 | 0.69 | 0.81 | 38 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1712 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1424 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1387 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1325 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 835 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6TIZ · Drosophila GDP-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 6TIZ · PDBe 6TIZ · UniProt P06603 · UniProt Q24560 · UniProt P63043
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