Research workbench
A new complex structure of tubulin with an alpha-beta unsaturated lactone
Analyse A new complex structure of tubulin with an alpha-beta unsaturated lactone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FNV
- Type
- protein
- Length
- 2,133 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; Tubulin tyrosine ligase
- UniProt
- Q2XVP4, P02554, P63043, E1BQ43
- Ligands
- GTP, GDP, X3H, ACP, MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 429 | 45% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 419 | 50% helix, 18% strand | P02554 |
| C | Tubulin alpha-1B chain | protein | 439 | 46% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 419 | 49% helix, 19% strand | P02554 |
| E | Stathmin-4 | protein | 119 | 76% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 308 | 28% helix, 23% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- X3H · Pironetin · ligand · chains 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
- 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.84 | 0.86 | 109 | GDP, MG, X3H |
| 2 | 1037 | 0.83 | 0.84 | 114 | GTP, MG |
| 3 | 1105 | 0.80 | 0.82 | 119 | GTP, MG |
| 4 | 158 | 0.76 | 0.93 | 33 | empty |
| 5 | 853 | 0.72 | 0.77 | 65 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1600 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1407 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1393 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1092 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 847 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5FNV · a new complex structure of tubulin with an alpha-beta unsaturated lactone · 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 Q2XVP4
- Every structure of UniProt P02554
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5FNV · PDBe 5FNV · UniProt Q2XVP4 · UniProt P02554 · UniProt P63043 · UniProt E1BQ43
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