MolNFT v1 · #161980 · protein
Ngckk (N.GRUBERI ckk) decorated 13PF taxol-GDP microtubule
6QUY · Tubulin alpha-1B chain: “Ngckk (N.GRUBERI ckk) decorated 13PF taxol-GDP microtubule”. Electron microscopy, 4 ligands (GTP, GDP, TA1), 20 pockets (best druggability 0.84). MolNFT v1 #161980 on GenesisL1: 3D structure, binding sites…
- PDB
- 6QUY
- Type
- protein
- Length
- 1,837 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Ckk domain protein; Tubulin beta chain
- UniProt
- P68363, D2VJG4, P07437
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tubulin alpha-1B chain | protein | 432 | 33% helix, 15% strand | P68363 |
| W | Ckk domain protein | protein | 113 | 20% helix, 22% strand | D2VJG4 |
| H, G | Tubulin beta chain | protein | 430 | 40% helix, 16% strand | P07437 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, H, C, G
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains H, G
- TA1 · Taxol · ligand · 2 copies · chains H, G
- MG · Magnesium ion · metal · 2 copies · chains A, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.84 | 0.95 | 43 | GTP, MG |
| 2 | 292 | 0.83 | 0.94 | 47 | GTP, MG |
| 3 | 1092 | 0.81 | 0.82 | 103 | empty |
| 4 | 580 | 0.73 | 0.81 | 58 | empty |
| 5 | 360 | 0.70 | 0.83 | 42 | empty |
Interfaces
8 interfaces between chains.
- C–G · 2076 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 2050 Ų buried · 17 hydrogen bonds · protein-protein
- W–H · 647 Ų buried · 12 hydrogen bonds · protein-protein
- W–G · 476 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6QUY · NgCKK (N.Gruberi CKK) decorated 13pf taxol-GDP microtubule · the same entry in another collection · chain C against C, TM-score 1.00
- 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 0.98
- P07437 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P07437) · a predicted model of the same protein · chain H against A, TM-score 0.96
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 D2VJG4
- Every structure of UniProt P07437
- Elsewhere: RCSB PDB 6QUY · PDBe 6QUY · UniProt P68363 · UniProt D2VJG4 · UniProt P07437
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