MolNFT v1 · #166546 · protein
Refined half-complex from tetradecameric assembly of thermococcus gammatolerans mcrb aaa+ hexamers with bound mcrc
6UT8 · GTPase subunit of restriction endonuclease: “Refined half-complex from tetradecameric assembly of thermococcus gammatolerans mcrb aaa+ hexamers with bound…”. Electron microscopy, 3 ligands (GSP, GDP, MG), 20 pockets (best…
- PDB
- 6UT8
- Type
- protein
- Length
- 2,761 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase subunit of restriction endonuclease; Mcrbc 5-methylcytosine restriction system…
- UniProt
- C5A3Z3, C5A3Z2
- Ligands
- GSP, GDP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | GTPase subunit of restriction endonuclease | protein | 390 | 43% helix, 12% strand | C5A3Z3 |
| B, E, F | GTPase subunit of restriction endonuclease | protein | 392 | 40% helix, 12% strand | C5A3Z3 |
| D | GTPase subunit of restriction endonuclease | protein | 391 | 37% helix, 11% strand | C5A3Z3 |
| G | Mcrbc 5-methylcytosine restriction system component | protein | 414 | 35% helix, 20% strand | C5A3Z2 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 4 copies · chains B, C, D, E, F
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.88 | 0.91 | 108 | empty |
| 2 | 1004 | 0.85 | 0.86 | 97 | GDP, MG |
| 3 | 1162 | 0.83 | 0.84 | 123 | empty |
| 4 | 571 | 0.83 | 0.88 | 56 | empty |
| 5 | 861 | 0.81 | 0.84 | 80 | empty |
Interfaces
12 interfaces between chains.
- D–E · 2972 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2834 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2811 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2682 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 2193 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6UT8 · Refined half-complex from tetradecameric assembly of Thermococcus gammatolerans McrB AAA+… · 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
- Every structure of UniProt C5A3Z2
- Elsewhere: RCSB PDB 6UT8 · PDBe 6UT8 · UniProt C5A3Z3 · UniProt C5A3Z2
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