Research workbench
Cryo-EM structure of the asymmetric aaa+ domain hexamer from thermococcus gammatolerans mcrb
Analyse Cryo-EM structure of the asymmetric aaa+ domain hexamer from thermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UT4
- Type
- protein
- Length
- 2,315 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase subunit of restriction endonuclease
- UniProt
- C5A3Z3
- Ligands
- GSP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase subunit of restriction endonuclease | protein | 387 | 38% helix, 14% strand | C5A3Z3 |
| B | GTPase subunit of restriction endonuclease | protein | 385 | 42% helix, 12% strand | C5A3Z3 |
| C | GTPase subunit of restriction endonuclease | protein | 384 | 43% helix, 13% strand | C5A3Z3 |
| D | GTPase subunit of restriction endonuclease | protein | 383 | 44% helix, 13% strand | C5A3Z3 |
| E | GTPase subunit of restriction endonuclease | protein | 386 | 42% helix, 13% strand | C5A3Z3 |
| F | GTPase subunit of restriction endonuclease | protein | 390 | 44% helix, 14% strand | C5A3Z3 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
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 | 1108 | 0.85 | 0.86 | 127 | GSP, MG |
| 2 | 1099 | 0.84 | 0.85 | 108 | empty |
| 3 | 1102 | 0.82 | 0.83 | 94 | GSP, MG |
| 4 | 905 | 0.82 | 0.84 | 82 | empty |
| 5 | 601 | 0.81 | 0.86 | 66 | empty |
Interfaces
6 interfaces between chains.
- D–E · 2703 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2678 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2668 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2525 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1866 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6UT4 · Cryo-EM structure of the asymmetric AAA+ domain hexamer from Thermococcus gammatolerans… · 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 C5A3Z3
- Elsewhere: RCSB PDB 6UT4 · PDBe 6UT4 · UniProt C5A3Z3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.