Research workbench
Structure of a trapped endonuclease III-DNA covalent intermediate: estranged-adenine complex
Analyse Structure of a trapped endonuclease III-DNA covalent intermediate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ORP
- Type
- protein + DNA
- Length
- 234 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*GP*AP*CP*AP*TP*GP*GP*AP*C)-3'; 5'-D(*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3'…
- Ligands
- SF4, NA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*GP*AP*CP*AP*TP*GP*GP*AP*C)-3' | dna | 11 | — | — |
| C | 5'-D(*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3' | dna | 10 | — | — |
| A | Endonuclease III | protein | 213 | 64% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.72 | 0.98 | 18 | empty |
| 2 | 61 | 0.52 | 0.87 | 14 | empty |
| 3 | 216 | 0.48 | 0.76 | 23 | empty |
| 4 | 116 | 0.37 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–A · 679 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 435 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- B–A · 385 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1ORP · Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Adenine… · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 1ORP · PDBe 1ORP
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