Research workbench
TUBULIN:STATHMIN-like domain complex
Analyse TUBULIN:STATHMIN-like domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FFX
- Type
- protein
- Length
- 1,757 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (tubulin); Protein (stathmin-like domain of RB3)
- UniProt
- P02550, P02554
- Ligands
- GTP, GDP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (tubulin) | protein | 423 | 25% helix, 8% strand | P02550 |
| B, D | Protein (tubulin) | protein | 410 | 25% helix, 12% strand | P02554 |
| E | Protein (stathmin-like domain of RB3) | protein | 91 | 57% helix, 0% strand | — |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.84 | 0.85 | 139 | GDP |
| 2 | 847 | 0.84 | 0.86 | 81 | GTP |
| 3 | 1161 | 0.83 | 0.84 | 103 | GTP |
| 4 | 676 | 0.76 | 0.81 | 66 | empty |
| 5 | 666 | 0.75 | 0.81 | 65 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1132 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1130 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1034 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 359 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 329 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1FFX · TUBULIN:STATHMIN-like domain complex · the same entry in another collection · chain B against B, TM-score 1.00
- P02554 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02554) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P02550 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (P02550) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P02550
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 1FFX · PDBe 1FFX · UniProt P02550 · UniProt P02554
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