Research workbench
Crystal structure of T2R-ttl-cevipabulin complex
Analyse Crystal structure of T2R-ttl-cevipabulin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CLD
- Type
- protein
- Length
- 2,196 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- Q2XVP4, A0A287AGU7, P63043, E1BQ43
- Ligands
- GTP, G2X, GDP, ACP, CA, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 438 | 46% helix, 19% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 418 | 48% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 18% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 426 | 48% helix, 19% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 123 | 63% helix, 11% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 351 | 31% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- G2X · 6-[2,6-bis(fluoranyl)-4-[3-(methylamino) propoxy]phenyl]-5-chloranyl-N-[(2S)-1,1,1-tris(fluoranyl)propan-2-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine · ligand · 2 copies · chains B, C
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- CA · Calcium ion · metal · 7 copies · chains A, E, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.84 | 0.86 | 83 | GDP, MG, G2X |
| 2 | 884 | 0.80 | 0.83 | 81 | GTP, MG, G2X |
| 3 | 1122 | 0.79 | 0.81 | 103 | MG, ACP |
| 4 | 162 | 0.79 | 0.95 | 33 | GTP, MG |
| 5 | 120 | 0.77 | 0.96 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1623 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1438 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1434 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1431 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 831 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7CLD · Crystal structure of T2R-TTL-Cevipabulin 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 Q2XVP4
- Every structure of UniProt A0A287AGU7
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 7CLD · PDBe 7CLD · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
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