MolNFT v1 · #2316 · protein + DNA
Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease
1BSU · DNA (5'-D(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3'): “Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction…”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.83). MolNFT…
- PDB
- 1BSU
- Type
- protein + DNA
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3'); DNA…
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- CA
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3') | dna | 10 | — | — |
| D | DNA (5'-D(*AP*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3') | dna | 11 | — | — |
| A | Endonuclease ecorv (3.1.21.4) (EC 3.1.21.4) | protein | 236 | 33% helix, 32% strand | P04390 |
| B | Endonuclease ecorv (3.1.21.4) (EC 3.1.21.4) | protein | 229 | 30% helix, 31% strand | P04390 |
Ligands and binding sites
- CA · Calcium 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.83 | 0.88 | 71 | empty |
| 2 | 179 | 0.55 | 0.80 | 27 | empty |
| 3 | 199 | 0.52 | 0.78 | 35 | empty |
| 4 | 109 | 0.44 | 0.78 | 22 | empty |
| 5 | 71 | 0.38 | 0.77 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1652 Ų buried · 17 hydrogen bonds · protein-protein
- C–A · 724 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–B · 704 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–B · 463 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–A · 453 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1BSU · Structural and energetic origins of indirect readout in site-specific DNA cleavage by a… · the same entry in another collection · chain C against C, TM-score 1.00
- P04390 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecorv (P04390) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P04390
- Elsewhere: RCSB PDB 1BSU · PDBe 1BSU · UniProt P04390
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