Research workbench
Crystal structure of tubulin-stathmin-ttl-thiocolchicine complex
Analyse Crystal structure of tubulin-stathmin-ttl-thiocolchicine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LP6
- Type
- protein
- Length
- 2,183 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; Uncharacterized protein
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, 71P, MG, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 439 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 422 | 48% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 18% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 421 | 47% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 121 | 76% helix, 12% strand | P63043 |
| F | Uncharacterized protein | protein | 340 | 30% 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
- 71P · ~{N}-[(7~{R})-1,2,3-trimethoxy-10-methylsulfanyl-9-oxidanylidene-6,7-dihydro-5~{H}-benzo[a]heptalen-7-yl]ethanamide · ligand · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B, E, C, D
- CA · Calcium ion · metal · chains C
- CL · Chloride ion · ion · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.86 | 0.94 | 64 | GTP, MG, 71P |
| 2 | 962 | 0.85 | 0.86 | 114 | GDP, MG |
| 3 | 1131 | 0.80 | 0.82 | 119 | GTP, MG |
| 4 | 186 | 0.77 | 0.92 | 46 | empty |
| 5 | 540 | 0.72 | 0.81 | 62 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1673 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1437 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 963 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 882 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5LP6 · Crystal structure of Tubulin-Stathmin-TTL-Thiocolchicine 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 5LP6 · PDBe 5LP6 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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