MolNFT v1 · #166543 · protein
Cryo-EM structure of the thermococcus gammatolerans mcrbc complex
6UT5 · GTPase subunit of restriction endonuclease: “Cryo-EM structure of the thermococcus gammatolerans mcrbc complex”. Electron microscopy, 3 ligands (GSP, GDP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #166543 on GenesisL1: 3D…
- PDB
- 6UT5
- Type
- protein
- Length
- 2,697 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 0.87
Structure
electron microscopy · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | GTPase subunit of restriction endonuclease | protein | 395 | 45% helix, 13% strand | C5A3Z3 |
| C | GTPase subunit of restriction endonuclease | protein | 393 | 44% helix, 13% strand | C5A3Z3 |
| G | Mcrbc 5-methylcytosine restriction system component | protein | 329 | 36% helix, 17% strand | C5A3Z2 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 5 copies · chains A, B, C, D, E, F
- GDP · Guanosine-5'-diphosphate · ligand · chains A, 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 | 1043 | 0.87 | 0.88 | 115 | empty |
| 2 | 938 | 0.86 | 0.88 | 113 | GDP, MG |
| 3 | 707 | 0.86 | 0.90 | 94 | GSP, MG |
| 4 | 1166 | 0.85 | 0.86 | 114 | empty |
| 5 | 976 | 0.81 | 0.83 | 86 | empty |
Interfaces
12 interfaces between chains.
- D–E · 2736 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2736 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2709 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2499 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 1938 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6UT5 · Cryo-EM structure of the Thermococcus gammatolerans McrBC complex · the same entry in another collection · chain B against B, 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 6UT5 · PDBe 6UT5 · UniProt C5A3Z3 · UniProt C5A3Z2
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