Research workbench
Crystal structure of TD1-mebendazole complex
Analyse Crystal structure of TD1-mebendazole complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ODN
- Type
- protein
- Length
- 1,007 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain; Designed ankyrin repeat protein (darpin) D1
- UniProt
- P81947, Q2T9S0
- Ligands
- GTP, GDP, V95, MG, SO4, CL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 426 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-3 chain | protein | 426 | 48% helix, 20% strand | Q2T9S0 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 54% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- V95 · methyl N-(6-benzoyl-1H-benzimidazol-2-yl)carbamate · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, F
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.82 | 0.83 | 116 | GTP, MG, SO4, V95, CL |
| 2 | 164 | 0.63 | 0.85 | 19 | empty |
| 3 | 185 | 0.62 | 0.83 | 36 | GDP |
| 4 | 129 | 0.55 | 0.82 | 29 | SO4 |
| 5 | 203 | 0.53 | 0.78 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1495 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 952 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 P81947
- Every structure of UniProt Q2T9S0
- Elsewhere: RCSB PDB 7ODN · PDBe 7ODN · UniProt P81947 · UniProt Q2T9S0
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