Research workbench
GDP-tubulin: RB3 stathmin-like domain complex
Analyse GDP-tubulin: RB3 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
- 3RYI
- Type
- protein
- Length
- 1,860 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-4
- UniProt
- D0VWZ0, D0VWY9, P63043
- Ligands
- GTP, GDP, MG, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 433 | 45% helix, 18% strand | D0VWZ0 |
| B, D | Tubulin beta chain | protein | 431 | 49% helix, 18% strand | D0VWY9 |
| C | Tubulin alpha chain | protein | 429 | 45% helix, 18% strand | D0VWZ0 |
| E | Stathmin-4 | protein | 136 | 69% helix, 13% strand | P63043 |
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
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E
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 | 1019 | 0.81 | 0.82 | 101 | GTP, MG, SO4 |
| 2 | 1124 | 0.80 | 0.82 | 119 | GDP, SO4 |
| 3 | 434 | 0.76 | 0.85 | 55 | GTP, MG |
| 4 | 534 | 0.69 | 0.79 | 52 | empty |
| 5 | 457 | 0.69 | 0.80 | 52 | SO4 |
Interfaces
7 interfaces between chains.
- A–E · 1827 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1407 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1402 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1303 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 854 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3RYI · GDP-Tubulin: rb3 stathmin-like domain 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 D0VWZ0
- Every structure of UniProt D0VWY9
- Every structure of UniProt P63043
- Elsewhere: RCSB PDB 3RYI · PDBe 3RYI · UniProt D0VWZ0 · UniProt D0VWY9 · UniProt P63043
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