Research workbench
Mspji restriction endonuclease - P21 form
Analyse Mspji restriction endonuclease - P21 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F0Q
- Type
- protein
- Length
- 1,800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease
- UniProt
- A3PUQ5
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Restriction endonuclease | protein | 452 | 33% helix, 27% strand | A3PUQ5 |
| C | Restriction endonuclease | protein | 449 | 31% helix, 26% strand | A3PUQ5 |
| D | Restriction endonuclease | protein | 447 | 31% helix, 26% strand | A3PUQ5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.86 | 0.95 | 79 | empty |
| 2 | 440 | 0.85 | 0.93 | 71 | empty |
| 3 | 305 | 0.82 | 0.93 | 57 | empty |
| 4 | 298 | 0.81 | 0.92 | 63 | empty |
| 5 | 397 | 0.79 | 0.88 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3898 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 1520 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1152 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1059 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 817 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4F0Q · MspJI Restriction Endonuclease - P21 Form · 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 A3PUQ5
- Elsewhere: RCSB PDB 4F0Q · PDBe 4F0Q · UniProt A3PUQ5
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