MolNFT v1 · #19625 · protein + DNA
The crystal structure of a post-reactive cognate DNA-eco ri complex at 2.50 a in the presence of MN2+ ion
1QPS · 5'-D(*TP*CP*GP*CP*GP*)-3': “The crystal structure of a post-reactive cognate DNA-eco ri complex at 2.50 a in the presence of MN2+ ion”. X-ray diffraction, 1 ligand (MN), 2 pockets (best druggability 0.35). MolNFT v1 #19625 on…
- PDB
- 1QPS
- Type
- protein + DNA
- Length
- 274 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*CP*GP*CP*GP*)-3'; 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3'; Endonuclease ecori
- UniProt
- P00642
- Ligands
- MN
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | 5'-D(*TP*CP*GP*CP*GP*)-3' | dna | 5 | — | — |
| N | 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3' | dna | 8 | — | — |
| A | Endonuclease ecori | protein | 261 | 34% helix, 20% strand | P00642 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains N, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.35 | 0.74 | 18 | empty |
| 2 | 75 | 0.34 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- N–A · 574 Ų buried · 14 hydrogen bonds · protein-nucleic
- M–A · 298 Ų buried · 8 hydrogen bonds · protein-nucleic
- M–N · 110 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 1QPS · The crystal structure of a post-reactive cognate DNA-eco ri complex at 2.50 a in the… · the same entry in another collection · chain M against M, TM-score 1.00
- P00642 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecori (P00642) · a predicted model of the same protein · chain A 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 P00642
- Elsewhere: RCSB PDB 1QPS · PDBe 1QPS · UniProt P00642
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