MolNFT v1 · #165079 · protein
Drosophila gmpcpp-tubulin
6TIY · Tubulin alpha-1 chain: “Drosophila gmpcpp-tubulin”. X-ray diffraction, 4 ligands (GTP, G2P, MG), 20 pockets (best druggability 0.81). MolNFT v1 #165079 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TIY
- Type
- protein
- Length
- 1,858 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, G2P, MG, SO4
- Pockets
- 20 · best druggability 0.81
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 | 434 | 45% helix, 18% strand | P06603 |
| B | Tubulin beta-1 chain | protein | 430 | 50% helix, 19% strand | Q24560 |
| C | Tubulin alpha-1 chain | protein | 434 | 45% helix, 18% strand | P06603 |
| D | Tubulin beta-1 chain | protein | 427 | 49% helix, 19% strand | Q24560 |
| E | Stathmin-4 | protein | 133 | 71% helix, 13% strand | P63043 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · chains A, E
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 | 666 | 0.81 | 0.86 | 83 | G2P, MG |
| 2 | 441 | 0.77 | 0.86 | 57 | GTP, MG |
| 3 | 414 | 0.77 | 0.86 | 55 | GTP, MG |
| 4 | 512 | 0.72 | 0.81 | 54 | empty |
| 5 | 441 | 0.68 | 0.80 | 42 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1817 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1434 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1431 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1347 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 830 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6TIY · Drosophila gmpcpp-tubulin · 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 D 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 6TIY · PDBe 6TIY · UniProt P06603 · UniProt Q24560 · UniProt P63043
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