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An asymmetric complex of restriction endonuclease mspi on its palindromic DNA recognition site
Analyse An asymmetric complex of restriction endonuclease mspi on its palindromic DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SA3
- Type
- protein + DNA
- Length
- 560 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
- Ligands
- NA
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3' | dna | 9 | — | — |
| D, F | 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3' | dna | 9 | — | — |
| A, B | Type II restriction enzyme mspi (EC 3.1.21.4) | protein | 262 | 44% helix, 22% strand | P11405 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.79 | 0.80 | 68 | empty |
| 2 | 359 | 0.61 | 0.78 | 32 | NA |
| 3 | 314 | 0.58 | 0.77 | 29 | NA |
| 4 | 242 | 0.55 | 0.78 | 21 | empty |
| 5 | 235 | 0.54 | 0.77 | 21 | empty |
Interfaces
11 interfaces between chains.
- C–A · 711 Ų buried · 19 hydrogen bonds · protein-nucleic
- E–B · 688 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–B · 552 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 546 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 439 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 1SA3 · An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition… · the same entry in another collection · chain B against B, 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 1SA3 · PDBe 1SA3 · UniProt P11405
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