MolNFT v1 · #81768 · protein + DNA
Crystal structure of type iif restriction endonuclease BSE634I with cognate DNA
3V20 · Endonuclease BSE634IR: “Crystal structure of type iif restriction endonuclease BSE634I with cognate DNA”. X-ray diffraction, 2 ligands (CA, CL), 7 pockets (best druggability 0.56). MolNFT v1 #81768 on GenesisL1: 3D structure…
- PDB
- 3V20
- Type
- protein + DNA
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease BSE634IR; DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
- EC
- 3.1.21.4
- UniProt
- Q8RT53
- Ligands
- CA, CL
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease BSE634IR (EC 3.1.21.4) | protein | 290 | 49% helix, 16% strand | Q8RT53 |
| B | Endonuclease BSE634IR (EC 3.1.21.4) | protein | 288 | 46% helix, 16% strand | Q8RT53 |
| C, D | DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · chains A
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.56 | 0.77 | 27 | 7PE |
| 2 | 225 | 0.55 | 0.78 | 21 | empty |
| 3 | 118 | 0.46 | 0.78 | 20 | empty |
| 4 | 79 | 0.36 | 0.76 | 14 | empty |
| 5 | 69 | 0.35 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–D · 732 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 705 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 406 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3V20 · Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA · 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 Q8RT53
- Elsewhere: RCSB PDB 3V20 · PDBe 3V20 · UniProt Q8RT53
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