Research workbench
Tubulin-eribulin complex
Analyse Tubulin-eribulin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JH7
- Type
- protein
- Length
- 2,194 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, 6K9, 03S, ACP, CA, MG
- Pockets
- 20 · best druggability 0.81
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 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 428 | 47% helix, 18% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 424 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 121 | 78% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 342 | 33% helix, 22% 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
- 6K9 · (1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one (non-preferred name) · ligand · 2 copies · chains B, C, D
- 03S · methanesulfonic acid · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- CA · Calcium ion · metal · 5 copies · chains A, B, C, E
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D, F
- IMD · Imidazole · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, E, C
- 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 | 215 | 0.81 | 0.95 | 41 | empty |
| 2 | 1026 | 0.81 | 0.82 | 111 | GDP, 6K9, 03S, GOL |
| 3 | 1077 | 0.80 | 0.81 | 110 | GTP, MG |
| 4 | 390 | 0.78 | 0.87 | 55 | GTP, MG |
| 5 | 892 | 0.76 | 0.80 | 79 | MG |
Interfaces
9 interfaces between chains.
- A–E · 1539 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1442 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 874 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 819 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5JH7 · Tubulin-Eribulin 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 5JH7 · PDBe 5JH7 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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