Research workbench
Tubulin-colchicine-vinblastine: stathmin-like domain complex
Analyse Tubulin-colchicine-vinblastine: stathmin-like domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z2B
- Type
- protein
- Length
- 1,816 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; RB3 stathmin-like domain 4
- UniProt
- P63043
- Ligands
- GTP, GDP, CN2, VLB, MG
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 427 | 43% helix, 15% strand | — |
| B, D | Tubulin beta chain | protein | 419 | 42% helix, 16% strand | — |
| C | Tubulin alpha chain | protein | 427 | 43% helix, 15% strand | — |
| E | RB3 stathmin-like domain 4 | protein | 124 | 33% helix, 4% strand | P63043 |
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
- CN2 · 2-mercapto-N-[1,2,3,10-tetramethoxy-9-oxo-5,6,7,9-tetrahydro-benzo[a]heptalen-7-yl]acetamide · ligand · 2 copies · chains A, B, C, D
- VLB · (2alpha,2'beta,3beta,4alpha,5beta)-vincaleukoblastine · ligand · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.85 | 0.87 | 94 | MG, GTP, CN2 |
| 2 | 831 | 0.83 | 0.86 | 114 | GDP, VLB |
| 3 | 1132 | 0.82 | 0.83 | 116 | MG, GTP, CN2 |
| 4 | 693 | 0.71 | 0.78 | 54 | empty |
| 5 | 132 | 0.70 | 0.91 | 30 | GDP |
Interfaces
7 interfaces between chains.
- A–E · 1528 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1296 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1253 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 842 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 746 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1Z2B · Tubulin-colchicine-vinblastine: stathmin-like domain 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 P63043
- Elsewhere: RCSB PDB 1Z2B · PDBe 1Z2B · UniProt P63043
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