Research workbench
Mutant (K220E) of the hsdr subunit of the ECOR124I restriction enzyme in complex with ATP
Analyse Mutant (K220E) 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
- 4BEB
- Type
- protein
- Length
- 3,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme hsdr
- EC
- 3.1.21.3
- UniProt
- Q304R3
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type I restriction enzyme hsdr (EC 3.1.21.3) | protein | 839 | 44% helix, 15% strand | Q304R3 |
| B | Type I restriction enzyme hsdr (EC 3.1.21.3) | protein | 842 | 44% helix, 15% strand | Q304R3 |
| C | Type I restriction enzyme hsdr (EC 3.1.21.3) | protein | 838 | 45% helix, 15% strand | Q304R3 |
| D | Type I restriction enzyme hsdr (EC 3.1.21.3) | protein | 833 | 44% helix, 15% strand | Q304R3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 966 | 0.81 | 0.83 | 85 | MG, ATP |
| 2 | 871 | 0.81 | 0.83 | 81 | MG, ATP |
| 3 | 858 | 0.81 | 0.83 | 74 | MG, ATP |
| 4 | 797 | 0.80 | 0.84 | 73 | MG, ATP |
| 5 | 196 | 0.74 | 0.90 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–C · 827 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 768 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 263 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4BEB · Mutant (K220E) of the hsdr subunit of the ECOR124I restriction enzyme in complex with ATP · 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 4BEB · PDBe 4BEB · UniProt Q304R3
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