MolNFT v1 · #81767 · protein + DNA
Crystal structure of type iif restriction endonuclease BSE634I with cognate DNA
3V1Z · Endonuclease BSE634IR: “Crystal structure of type iif restriction endonuclease BSE634I with cognate DNA”. X-ray diffraction, 6 pockets (best druggability 0.55). MolNFT v1 #81767 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3V1Z
- Type
- protein + DNA
- Length
- 605 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*GP*CP*CP*GP*GP*CP*GP*CP*G)-3')
- EC
- 3.1.21.4
- UniProt
- Q8RT53
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease BSE634IR (EC 3.1.21.4) | protein | 290 | 46% helix, 16% strand | Q8RT53 |
| B | Endonuclease BSE634IR (EC 3.1.21.4) | protein | 289 | 46% helix, 16% strand | Q8RT53 |
| C, D | DNA (5'-D(*TP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP*G)-3') | dna | 13 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.55 | 0.78 | 22 | empty |
| 2 | 245 | 0.55 | 0.77 | 26 | empty |
| 3 | 161 | 0.44 | 0.74 | 24 | empty |
| 4 | 114 | 0.44 | 0.77 | 23 | empty |
| 5 | 113 | 0.38 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 737 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 723 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 400 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3V1Z · 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 3V1Z · PDBe 3V1Z · UniProt Q8RT53
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