Research workbench
Crystal structure of tubulin with 17a
Analyse Crystal structure of tubulin with 17a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VMJ
- Type
- protein
- Length
- 2,190 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Bos taurus; Gallus gallus; Rattus norvegicus
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, 7PU, MG, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.9 · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 44% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 424 | 49% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 420 | 51% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 75% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 346 | 32% 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
- 7PU · N-[3-[[6-[[3-[bis(fluoranyl)methyl]phenyl]amino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains A
- 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 | 952 | 0.86 | 0.87 | 108 | GTP, MG |
| 2 | 930 | 0.84 | 0.86 | 118 | GDP, MG |
| 3 | 1050 | 0.83 | 0.84 | 103 | GTP, MG |
| 4 | 159 | 0.78 | 0.94 | 35 | 7PU |
| 5 | 1072 | 0.77 | 0.79 | 92 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1663 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1413 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1365 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 873 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 817 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- P81947 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P81947) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 7VMJ · PDBe 7VMJ · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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