Research workbench
Crystal structure of the hsdr subunit of the ECOR124I restriction enzyme with the C-terminal domain
Analyse Crystal structure of the hsdr subunit of the ECOR124I restriction enzyme with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H2J
- Type
- protein
- Length
- 1,832 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme R protein
- EC
- 3.1.21.3
- UniProt
- Q304R3
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 842 | 46% helix, 15% strand | Q304R3 |
| B | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 990 | 48% helix, 13% strand | Q304R3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.82 | 0.85 | 83 | ATP, MG |
| 2 | 721 | 0.82 | 0.86 | 83 | ATP, MG |
| 3 | 134 | 0.74 | 0.93 | 28 | empty |
| 4 | 648 | 0.73 | 0.80 | 66 | empty |
| 5 | 134 | 0.73 | 0.92 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 820 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 6H2J · Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme with the… · 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 Q304R3
- Elsewhere: RCSB PDB 6H2J · PDBe 6H2J · UniProt Q304R3
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