MolNFT v1 · #166545 · protein
Fitted model for the tetradecameric assembly of thermococcus gammatolerans mcrb aaa+ hexamers with bound mcrc
6UT7 · GTPase subunit of restriction endonuclease: “Fitted model for the tetradecameric assembly of thermococcus gammatolerans mcrb aaa+ hexamers with bound mcrc”. Electron microscopy, 3 ligands (GSP, GDP, MG), 20 pockets (best…
- PDB
- 6UT7
- Type
- protein
- Length
- 5,522 residues
- Chains
- 14
- 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, H, J | GTPase subunit of restriction endonuclease | protein | 390 | 43% helix, 12% strand | C5A3Z3 |
| B, E, F, I, L, M | GTPase subunit of restriction endonuclease | protein | 392 | 40% helix, 12% strand | C5A3Z3 |
| D, K | GTPase subunit of restriction endonuclease | protein | 391 | 37% helix, 11% strand | C5A3Z3 |
| G, N | Mcrbc 5-methylcytosine restriction system component | protein | 414 | 35% helix, 20% strand | C5A3Z2 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 8 copies · chains B, C, D, E, F, I, J, K, L, M
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, F, H, I, M
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, H, I, J, K, L, M
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 | 842 | 0.88 | 0.91 | 107 | empty |
| 2 | 1039 | 0.85 | 0.86 | 102 | GDP, MG |
| 3 | 877 | 0.85 | 0.87 | 106 | empty |
| 4 | 867 | 0.84 | 0.86 | 101 | empty |
| 5 | 507 | 0.83 | 0.90 | 58 | empty |
Interfaces
25 interfaces between chains.
- D–E · 2968 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 2968 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2840 Ų buried · 19 hydrogen bonds · protein-protein
- L–M · 2834 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2817 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6UT7 · Fitted model for the 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 6UT7 · PDBe 6UT7 · UniProt C5A3Z3 · UniProt C5A3Z2
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