MolNFT v1 · #28480 · protein + DNA
Crystal structure of restriction endonuclease mspi in complex with its cognate DNA in P212121 space group
1YFI · 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3': “Crystal structure of restriction endonuclease mspi in complex with its cognate DNA in P212121 space group”. X-ray diffraction, 8 pockets (best druggability 0.74). MolNFT v1 #28480 on…
- PDB
- 1YFI
- Type
- protein + DNA
- Length
- 562 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'; Type II restriction enzyme mspi
- EC
- 3.1.21.4
- UniProt
- P11405
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3' | dna | 9 | — | — |
| D | 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3' | dna | 9 | — | — |
| E, F | 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3' | dna | 10 | — | — |
| A, B | Type II restriction enzyme mspi (EC 3.1.21.4) | protein | 262 | 43% helix, 22% strand | P11405 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.74 | 0.85 | 46 | empty |
| 2 | 474 | 0.68 | 0.80 | 47 | empty |
| 3 | 606 | 0.68 | 0.78 | 48 | empty |
| 4 | 290 | 0.68 | 0.83 | 29 | empty |
| 5 | 241 | 0.53 | 0.77 | 32 | empty |
Interfaces
15 interfaces between chains.
- E–B · 690 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 689 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–B · 664 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 565 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–F · 484 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 1YFI · Crystal Structure of restriction endonuclease MspI in complex with its cognate DNA in… · the same entry in another collection · chain E against E, TM-score 1.00
- P11405 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme mspi (P11405) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P11405
- Elsewhere: RCSB PDB 1YFI · PDBe 1YFI · UniProt P11405
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