Research workbench
Mutant (K220R) of the hsdr subunit of the ECOR124I restriction enzyme in complex with ATP
Analyse Mutant (K220R) of the hsdr subunit of the ECOR124I restriction enzyme in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BE7
- Type
- protein
- Length
- 1,672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme ECOR124II R protein
- EC
- 3.1.21.3
- UniProt
- Q304R3
- Ligands
- ATP, MG, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Type I restriction enzyme ECOR124II R protein (EC 3.1.21.3) | protein | 837 | 45% helix, 15% strand | Q304R3 |
| D | Type I restriction enzyme ECOR124II R protein (EC 3.1.21.3) | protein | 835 | 44% helix, 15% strand | Q304R3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 4 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.83 | 0.88 | 68 | ATP, MG |
| 2 | 725 | 0.82 | 0.86 | 80 | MG, ATP |
| 3 | 609 | 0.72 | 0.80 | 54 | empty |
| 4 | 626 | 0.71 | 0.79 | 53 | empty |
| 5 | 191 | 0.71 | 0.88 | 39 | empty |
Interfaces
1 interface between chains.
- B–D · 847 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4BE7 · Mutant (K220R) of the hsdr subunit of the ECOR124I restriction enzyme in complex with ATP · 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 Q304R3
- Elsewhere: RCSB PDB 4BE7 · PDBe 4BE7 · UniProt Q304R3
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