MolNFT v1 · #122884 · protein
Tubulin-vinblastine complex
5J2T · Tubulin alpha-1B chain: “Tubulin-vinblastine complex”. X-ray diffraction, 5 ligands (GTP, GDP, VLB), 20 pockets (best druggability 0.81). MolNFT v1 #122884 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5J2T
- Type
- protein
- Length
- 2,182 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, VLB, 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 | 45% helix, 18% strand | P81947 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 18% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 424 | 49% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 120 | 77% helix, 13% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 331 | 29% helix, 21% strand | E1BQ43 |
| B | Tubulin beta-2B chain | protein | 428 | 48% helix, 18% strand | Q6B856 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains D, B
- VLB · (2alpha,2'beta,3beta,4alpha,5beta)-vincaleukoblastine · ligand · chains C, B
- MG · Magnesium ion · metal · 3 copies · chains A, C, D, B
- CA · Calcium ion · metal · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.81 | 0.83 | 115 | VLB, GDP, MG |
| 2 | 1024 | 0.81 | 0.82 | 114 | GTP, MG |
| 3 | 209 | 0.81 | 0.95 | 44 | empty |
| 4 | 873 | 0.79 | 0.82 | 97 | GTP, MG |
| 5 | 975 | 0.76 | 0.79 | 83 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1541 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1399 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1383 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 904 Ų buried · 13 hydrogen bonds · protein-protein
- C–B · 879 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5J2T · Tubulin-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 Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5J2T · PDBe 5J2T · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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