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Crystal structure of restriction endonuclease mspi in complex with its cognate DNA in P212121 space group
Analyse Crystal structure of restriction endonuclease mspi in complex with its cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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