MolNFT v1 · #105347 · protein + DNA
Mspji restriction endonuclease in complex with 27-mer oligonucleotide
4R28: “Mspji restriction endonuclease in complex with 27-mer oligonucleotide”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #105347 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4R28
- Type
- protein + DNA
- Length
- 1,845 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease; DNA (25-mer); DNA (26-mer)
- UniProt
- A3PUQ5
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Restriction endonuclease | protein | 449 | 30% helix, 23% strand | A3PUQ5 |
| B | Restriction endonuclease | protein | 447 | 29% helix, 25% strand | A3PUQ5 |
| X | DNA (25-mer) | dna | 25 | — | — |
| Y | DNA (26-mer) | dna | 26 | — | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.89 | 0.91 | 144 | empty |
| 2 | 1139 | 0.88 | 0.89 | 145 | empty |
| 3 | 1139 | 0.86 | 0.87 | 131 | empty |
| 4 | 192 | 0.80 | 0.95 | 38 | empty |
| 5 | 154 | 0.77 | 0.94 | 28 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3964 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 1607 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1218 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1156 Ų buried · 21 hydrogen bonds · protein-protein
- X–Y · 1148 Ų buried · 118 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
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 4R28 · PDBe 4R28 · UniProt A3PUQ5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.