Research workbench
Crystal structure of T2R-ttl-lexibulin complex
Analyse Crystal structure of T2R-ttl-lexibulin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CA0
- Type
- protein
- Length
- 2,179 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Uncharacterized protein; Stathmin-4
- UniProt
- Q2XVP4, F2Z5B2, P63043, E1BQ43
- Ligands
- GTP, GDP, LXL, ACP, MG, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 19% strand | Q2XVP4 |
| B | Uncharacterized protein | protein | 426 | 46% helix, 19% strand | F2Z5B2 |
| C | Tubulin alpha-1B chain | protein | 440 | 45% helix, 17% strand | Q2XVP4 |
| D | Uncharacterized protein | protein | 421 | 49% helix, 19% strand | F2Z5B2 |
| E | Stathmin-4 | protein | 121 | 76% helix, 13% strand | P63043 |
| F | Uncharacterized protein | protein | 334 | 31% helix, 21% 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
- LXL · 1-ethyl-3-[2-methoxy-4-(5-methyl-4-{[(1S)-1-(pyridin-3-yl)butyl]amino}pyrimidin-2-yl)phenyl]urea · ligand · 2 copies · chains A, B, C, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · chains A
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.85 | 0.88 | 103 | GTP, MG, LXL |
| 2 | 1139 | 0.85 | 0.86 | 116 | GTP, MG, LXL |
| 3 | 671 | 0.82 | 0.87 | 88 | GDP, MG |
| 4 | 166 | 0.79 | 0.95 | 37 | empty |
| 5 | 71 | 0.72 | 0.97 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1576 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1521 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1396 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 904 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 816 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5CA0 · Crystal structure of T2R-TTL-Lexibulin 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 F2Z5B2
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5CA0 · PDBe 5CA0 · UniProt Q2XVP4 · UniProt F2Z5B2 · UniProt P63043 · UniProt E1BQ43
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