Research workbench
Closed conformation of the yeast wild-type gamma-turc
Analyse Closed conformation of the yeast wild-type gamma-turc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M2Y
- Type
- protein
- Length
- 2,278 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin gamma chain; Spindle pole body component SPC98; Spindle pole body component…
- UniProt
- P53378, P53540, P38863, P32380
- Ligands
- GDP
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin gamma chain | protein | 441 | 44% helix, 15% strand | P53378 |
| B | Tubulin gamma chain | protein | 447 | 42% helix, 15% strand | P53378 |
| C | Spindle pole body component SPC98 | protein | 656 | 64% helix, 4% strand | P53540 |
| D | Spindle pole body component SPC97 | protein | 703 | 62% helix, 5% strand | P38863 |
| U | Spindle pole body component 110 | protein | 31 | 68% helix, 0% strand | P32380 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.83 | 0.84 | 107 | empty |
| 2 | 168 | 0.82 | 0.97 | 36 | empty |
| 3 | 133 | 0.81 | 0.98 | 22 | empty |
| 4 | 115 | 0.80 | 0.98 | 21 | empty |
| 5 | 94 | 0.79 | 0.99 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3940 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 2863 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2512 Ų buried · 26 hydrogen bonds · protein-protein
- D–U · 605 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 372 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7M2Y · Closed conformation of the Yeast wild-type gamma-TuRC · the same entry in another collection · chain U against U, TM-score 1.00
- P53378 · AlphaFold monomer V2.0 prediction for tubulin gamma chain (P53378) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P38863 · AlphaFold monomer V2.0 prediction for spindle pole body component SPC97 (P38863) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P53540 · AlphaFold monomer V2.0 prediction for spindle pole body component SPC98 (P53540) · a predicted model of the same protein · chain C against A, TM-score 0.91
- P32380 · AlphaFold monomer V2.0 prediction for spindle pole body component 110 (P32380) · a predicted model of the same protein · chain U against A, TM-score 0.66
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 P53378
- Every structure of UniProt P53540
- Every structure of UniProt P38863
- Every structure of UniProt P32380
- Elsewhere: RCSB PDB 7M2Y · PDBe 7M2Y · UniProt P53378 · UniProt P53540 · UniProt P38863 · UniProt P32380
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