Research workbench
A TOG:ALPHA/BETA-tubulin complex structure reveals conformation-based mechanisms for a microtubule polymerase
Analyse A TOG:ALPHA/BETA-tubulin complex structure reveals conformation-based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FFB
- Type
- protein
- Length
- 1,087 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1 chain; Tubulin beta chain; Protein STU2
- EC
- 3.6.5.6
- UniProt
- P09733, P02557, P46675
- Ligands
- GTP, MG
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1 chain | protein | 435 | 42% helix, 18% strand | P09733 |
| B | Tubulin beta chain (EC 3.6.5.6) | protein | 421 | 47% helix, 18% strand | P02557 |
| C | Protein STU2 | protein | 231 | 69% helix, 0% strand | P46675 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.78 | 0.81 | 82 | MG, GTP |
| 2 | 577 | 0.69 | 0.78 | 52 | empty |
| 3 | 423 | 0.68 | 0.80 | 49 | empty |
| 4 | 263 | 0.62 | 0.80 | 34 | MG, GTP |
| 5 | 83 | 0.57 | 0.87 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1404 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 464 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 364 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4FFB · A TOG:alpha/beta-tubulin Complex Structure Reveals Conformation-Based Mechanisms For a… · the same entry in another collection · chain A against A, TM-score 1.00
- P02557 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02557) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P46675 · AlphaFold monomer V2.0 prediction for protein STU2 (P46675) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P09733 · AlphaFold monomer V2.0 prediction for tubulin alpha-1 chain (P09733) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P09733
- Every structure of UniProt P02557
- Every structure of UniProt P46675
- Elsewhere: RCSB PDB 4FFB · PDBe 4FFB · UniProt P09733 · UniProt P02557 · UniProt P46675
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