MolNFT v2 · #168004 · protein
Cryo-EM structure of the Escherichia coli McrBC complex
6UT6 · 5-methylcytosine-specific restriction enzyme B: “Cryo-EM structure of the Escherichia coli McrBC complex”. Electron microscopy at 3.28, 3 ligands (GSP, GDP, MG), 20 pockets (best druggability 0.85). MolNFT v2 #168004 on GenesisL1…
- PDB
- 6UT6
- Type
- protein
- Length
- 2,078 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.28
- Source
- Escherichia coli (strain K12)
- Molecule
- 5-methylcytosine-specific restriction enzyme B; Protein McrC
- EC
- 3.1.21.-
- UniProt
- P15005, P15006
- Ligands
- GSP, GDP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.28 · 4 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 288 | 42% helix, 16% strand | P15005 |
| C | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 287 | 37% helix, 16% strand | P15005 |
| D, E, F | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 292 | 39% helix, 14% strand | P15005 |
| G | Protein McrC | protein | 339 | 36% helix, 16% strand | P15006 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 5 copies · chains B, C, D, E, F, A
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains 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 | 972 | 0.85 | 0.86 | 119 | empty |
| 2 | 1166 | 0.84 | 0.85 | 143 | empty |
| 3 | 1004 | 0.81 | 0.82 | 81 | GSP |
| 4 | 1170 | 0.80 | 0.81 | 92 | GDP |
| 5 | 720 | 0.76 | 0.81 | 56 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2036 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2013 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1749 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1647 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1217 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6UT6 · Cryo-EM structure of the escherichia COLI mcrbc complex · the same entry in another collection · chain G against G, TM-score 1.00
- P15005 · AlphaFold monomer V2.0 prediction for 5-methylcytosine-specific restriction enzyme B… · a predicted model of the same protein · chain D against A, TM-score 0.99
- P15006 · AlphaFold monomer V2.0 prediction for protein mcrc (P15006) · a predicted model of the same protein · chain G against A, TM-score 0.90
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 P15005
- Every structure of UniProt P15006
- Elsewhere: RCSB PDB 6UT6 · PDBe 6UT6 · UniProt P15005 · UniProt P15006
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