MolNFT v1 · #114349 · protein
Crystal structure of tubulin-stathmin-ttl-vinblastine complex
5BMV · Tubulin alpha-1B chain: “Crystal structure of tubulin-stathmin-ttl-vinblastine complex”. X-ray diffraction, 6 ligands (GTP, GDP, VLB), 20 pockets (best druggability 0.81). MolNFT v1 #114349 on GenesisL1: 3D structure, binding sites…
- PDB
- 5BMV
- Type
- protein
- Length
- 2,197 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Uncharacterized protein
- UniProt
- P81947, P02554, P63043, E1BQ43
- Ligands
- GTP, GDP, VLB, ACP, MG, CA
- 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 chain | protein | 427 | 47% helix, 19% strand | P02554 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 17% strand | P81947 |
| D | Tubulin beta chain | protein | 422 | 49% helix, 19% strand | P02554 |
| E | Stathmin-4 | protein | 123 | 76% helix, 12% strand | P63043 |
| F | Uncharacterized protein | protein | 346 | 30% helix, 20% 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
- VLB · (2alpha,2'beta,3beta,4alpha,5beta)-vincaleukoblastine · ligand · chains B, C
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains A, E, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.81 | 0.83 | 105 | GTP, MG, GOL |
| 2 | 1140 | 0.81 | 0.83 | 120 | GDP, MG, VLB |
| 3 | 1081 | 0.81 | 0.82 | 125 | GTP, MG, GOL |
| 4 | 134 | 0.77 | 0.95 | 28 | empty |
| 5 | 1156 | 0.74 | 0.77 | 80 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1647 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1396 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 963 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 857 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5BMV · CRYSTAL STRUCTURE OF TUBULIN-STATHMIN-TTL-Vinblastine 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 P02554
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5BMV · PDBe 5BMV · UniProt P81947 · UniProt P02554 · UniProt P63043 · UniProt E1BQ43
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