MolNFT v1 · #3683 · protein + DNA
Crystal structure of muni restriction endonuclease in complex with cognate DNA
1D02 · DNA (5'-D(*GP*CP*CP*AP*AP*TP*TP*GP*GP*C)-3'): “Crystal structure of muni restriction endonuclease in complex with cognate DNA”. X-ray diffraction, 5 pockets (best druggability 0.52). MolNFT v1 #3683 on GenesisL1: 3D structure…
- PDB
- 1D02
- Type
- protein + DNA
- Length
- 417 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*CP*AP*AP*TP*TP*GP*GP*C)-3'); Type II restriction enzyme muni
- EC
- 3.1.21.4
- UniProt
- P43642
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*GP*CP*CP*AP*AP*TP*TP*GP*GP*C)-3') | dna | 10 | — | — |
| A | Type II restriction enzyme muni (EC 3.1.21.4) | protein | 197 | 41% helix, 14% strand | P43642 |
| B | Type II restriction enzyme muni (EC 3.1.21.4) | protein | 200 | 43% helix, 15% strand | P43642 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.52 | 0.77 | 24 | empty |
| 2 | 154 | 0.49 | 0.77 | 18 | empty |
| 3 | 195 | 0.48 | 0.75 | 22 | empty |
| 4 | 131 | 0.48 | 0.79 | 16 | empty |
| 5 | 118 | 0.38 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2253 Ų buried · 22 hydrogen bonds · protein-protein
- D–A · 660 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–B · 622 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 466 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- C–A · 246 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1D02 · Crystal structure of muni restriction endonuclease in complex with cognate DNA · the same entry in another collection · chain C against C, TM-score 1.00
- P43642 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme muni (P43642) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P43642
- Elsewhere: RCSB PDB 1D02 · PDBe 1D02 · UniProt P43642
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