MolNFT v1 · #3766 · protein + DNA
Crystal structure of restriction endonuclease bglii complexed with DNA 16-mer
1D2I · DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)…: “Crystal structure of restriction endonuclease bglii complexed with DNA 16-mer”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.69). MolNFT v1 #3766 on…
- PDB
- 1D2I
- Type
- protein + DNA
- Length
- 473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)- 3'); Protein (restriction…
- UniProt
- Q45488
- Ligands
- MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)- 3') | dna | 16 | — | — |
| A | Protein (restriction endonuclease bglii) | protein | 223 | 30% helix, 33% strand | Q45488 |
| B | Protein (restriction endonuclease bglii) | protein | 218 | 32% helix, 33% strand | Q45488 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.69 | 0.80 | 53 | empty |
| 2 | 255 | 0.67 | 0.84 | 28 | empty |
| 3 | 226 | 0.59 | 0.80 | 32 | empty |
| 4 | 150 | 0.53 | 0.81 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1135 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 921 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–A · 910 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–A · 689 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 627 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 1D2I · Crystal structure of restriction endonuclease bglii complexed with DNA 16-mer · the same entry in another collection · chain C against C, TM-score 1.00
- Q45488 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme bglii (Q45488) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q45488
- Elsewhere: RCSB PDB 1D2I · PDBe 1D2I · UniProt Q45488
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