MolNFT v1 · #165030 · protein
Tubulin-inhibitor complex
6TH4 · Tubulin alpha chain: “Tubulin-inhibitor complex”. X-ray diffraction, 5 ligands (GTP, GDP, N9B), 20 pockets (best druggability 0.84). MolNFT v1 #165030 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TH4
- Type
- protein
- Length
- 1,847 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-4
- UniProt
- P63043
- Ligands
- GTP, GDP, N9B, MG, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 428 | 47% helix, 18% strand | — |
| B | Tubulin beta chain | protein | 428 | 49% helix, 19% strand | — |
| C | Tubulin alpha chain | protein | 434 | 45% helix, 18% strand | — |
| D | Tubulin beta chain | protein | 429 | 50% helix, 19% strand | — |
| E | Stathmin-4 | protein | 128 | 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
- N9B · 1,2,3,9-tetramethoxy-6-methylidene-5~{H}-cyclohepta[a]naphthalen-8-one · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.84 | 0.89 | 88 | GTP, MG, N9B |
| 2 | 899 | 0.83 | 0.85 | 96 | GTP, MG, N9B |
| 3 | 732 | 0.81 | 0.85 | 91 | GDP |
| 4 | 530 | 0.71 | 0.80 | 80 | empty |
| 5 | 686 | 0.70 | 0.78 | 50 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1802 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1426 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1390 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1345 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 821 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6TH4 · Tubulin-inhibitor 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 P63043
- Elsewhere: RCSB PDB 6TH4 · PDBe 6TH4 · UniProt P63043
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