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Crystal structure of the restriction endonuclease bgli (E.C.3.1.21.4) bound to its DNA recognition sequence
Analyse Crystal structure of the restriction endonuclease bgli (E.C.3.1.21.4) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DMU
- Type
- protein + DNA
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3'); Bgli restriction…
- EC
- 3.1.21.4
- UniProt
- O68557
- Ligands
- CA
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | DNA (5'- D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3') | dna | 17 | — | — |
| A | Bgli restriction endonuclease (EC 3.1.21.4) | protein | 299 | 33% helix, 25% strand | O68557 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.51 | 0.75 | 24 | empty |
| 2 | 55 | 0.39 | 0.80 | 17 | empty |
| 3 | 62 | 0.32 | 0.75 | 13 | empty |
| 4 | 70 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- F–A · 930 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 1DMU · Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna… · the same entry in another collection · chain F against F, TM-score 1.00
- O68557 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme bgli (O68557) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O68557
- Elsewhere: RCSB PDB 1DMU · PDBe 1DMU · UniProt O68557
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