Research workbench
Crystal structure of T2R-ttl-nocodazole complex
Analyse Crystal structure of T2R-ttl-nocodazole complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CA1
- Type
- protein
- Length
- 2,180 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha; Tubulin beta-2 chain; Stathmin-4; Uncharacterized protein
- UniProt
- P32882, P63043, E1BQ43
- Ligands
- GTP, GDP, NZO, ACP, MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha | protein | 437 | 47% helix, 19% strand | — |
| B | Tubulin beta-2 chain | protein | 427 | 47% helix, 19% strand | P32882 |
| C | Tubulin alpha | protein | 440 | 45% helix, 17% strand | — |
| D | Tubulin beta-2 chain | protein | 421 | 48% helix, 18% strand | P32882 |
| E | Stathmin-4 | protein | 121 | 76% helix, 13% strand | P63043 |
| F | Uncharacterized protein | protein | 334 | 29% 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
- NZO · nocodazole · 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
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.84 | 0.87 | 109 | GTP, MG, NZO |
| 2 | 944 | 0.83 | 0.85 | 114 | GDP, MG |
| 3 | 1116 | 0.82 | 0.83 | 138 | GTP, MG, NZO |
| 4 | 151 | 0.78 | 0.95 | 30 | empty |
| 5 | 83 | 0.72 | 0.96 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1573 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1477 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1460 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 909 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 837 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- P32882 · AlphaFold monomer V2.0 prediction for tubulin beta-2 chain (P32882) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P32882
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5CA1 · PDBe 5CA1 · UniProt P32882 · UniProt P63043 · UniProt E1BQ43
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