MolNFT v1 · #150507 · protein
TUBULIN:TM-3 darpin complex
6GVN · Tubulin alpha chain: “TUBULIN:TM-3 darpin complex”. X-ray diffraction, 3 ligands (GTP, MG, SO4), 13 pockets (best druggability 0.80). MolNFT v1 #150507 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GVN
- Type
- protein
- Length
- 993 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Tm-3 darpin
- UniProt
- D0VWZ0, D0VWY9
- Ligands
- GTP, MG, SO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 434 | 46% helix, 17% strand | D0VWZ0 |
| B | Tubulin beta chain | protein | 431 | 49% helix, 19% strand | D0VWY9 |
| F | Tm-3 darpin | protein | 128 | 54% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains B, F
- 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
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.80 | 0.84 | 81 | GTP, MG |
| 2 | 195 | 0.61 | 0.83 | 36 | GTP, MG |
| 3 | 69 | 0.57 | 0.88 | 18 | empty |
| 4 | 52 | 0.54 | 0.90 | 16 | empty |
| 5 | 154 | 0.52 | 0.79 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1535 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 666 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GVN · Tubulin:TM-3 DARPin complex · the same entry in another collection · chain A against A, TM-score 1.00
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 D0VWZ0
- Every structure of UniProt D0VWY9
- Elsewhere: RCSB PDB 6GVN · PDBe 6GVN · UniProt D0VWZ0 · UniProt D0VWY9
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