MolNFT v1 · #161996 · protein
Ngckk (naegleria gruberi ckk) decorated 14PF taxol-GDP microtubule
6QVE · Tubulin alpha-1B chain: “Ngckk (naegleria gruberi ckk) decorated 14PF taxol-GDP microtubule”. Electron microscopy, 4 ligands (GTP, GDP, TA1), 20 pockets (best druggability 0.84). MolNFT v1 #161996 on GenesisL1: 3D structure, binding…
- PDB
- 6QVE
- Type
- protein
- Length
- 1,831 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Predicted protein; BETA1-tubulin
- UniProt
- P68363, D2VJG4, A0A2K5HGL3
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Tubulin alpha-1B chain | protein | 432 | 32% helix, 16% strand | P68363 |
| W | Predicted protein | protein | 107 | 19% helix, 29% strand | D2VJG4 |
| H, G | BETA1-tubulin | protein | 430 | 38% helix, 16% strand | A0A2K5HGL3 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, G, A, H
- 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 C, G, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.84 | 0.95 | 45 | GTP, MG |
| 2 | 274 | 0.83 | 0.94 | 41 | GTP, MG |
| 3 | 727 | 0.77 | 0.82 | 67 | empty |
| 4 | 430 | 0.75 | 0.85 | 49 | empty |
| 5 | 638 | 0.71 | 0.79 | 57 | empty |
Interfaces
8 interfaces between chains.
- C–G · 2094 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 2065 Ų buried · 17 hydrogen bonds · protein-protein
- W–H · 663 Ų buried · 6 hydrogen bonds · protein-protein
- C–A · 495 Ų buried · 3 hydrogen bonds · protein-protein
- W–G · 494 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6QVE · NgCKK (Naegleria Gruberi CKK) decorated 14pf 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 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 P68363
- Every structure of UniProt D2VJG4
- Every structure of UniProt A0A2K5HGL3
- Elsewhere: RCSB PDB 6QVE · PDBe 6QVE · UniProt P68363 · UniProt D2VJG4 · UniProt A0A2K5HGL3
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