Research workbench
Crystal structure of T2R-ttl -mebendazole complex
Analyse Crystal structure of T2R-ttl -mebendazole complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OGN
- Type
- protein
- Length
- 2,171 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin-tyrosine ligase
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, V95, ACP, MG, CA, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 439 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 421 | 48% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 48% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 422 | 48% helix, 20% strand | Q6B856 |
| E | Stathmin-4 | protein | 120 | 78% helix, 12% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 329 | 32% helix, 23% strand | E1BQ43 |
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
- V95 · methyl N-(6-benzoyl-1H-benzimidazol-2-yl)carbamate · ligand · 2 copies · chains A, B, C, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A, F
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 4 copies · chains A, B, C, E
- CL · Chloride ion · ion · 2 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
- IMD · Imidazole · additive · chains C
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 | 1175 | 0.87 | 0.88 | 151 | GTP, MG, V95 |
| 2 | 1180 | 0.82 | 0.83 | 125 | GDP, MG |
| 3 | 1113 | 0.79 | 0.81 | 116 | GTP, MG, V95 |
| 4 | 81 | 0.73 | 0.96 | 21 | empty |
| 5 | 426 | 0.72 | 0.83 | 61 | MES |
Interfaces
9 interfaces between chains.
- A–E · 1557 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1450 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1073 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 928 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7OGN · Crystal structure of T2R-TTL -mebendazole 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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 7OGN · PDBe 7OGN · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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