Research workbench
Crystal structure of endonuclease Q complex with 27-mer duplex substrate with an abasic lesion at the active site
Analyse Crystal structure of endonuclease Q complex with 27-mer duplex substrate with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K32
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease Q; DNA (27-mer)
- UniProt
- I6V2I0
- Ligands
- ZN, MG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease Q | protein | 395 | 34% helix, 17% strand | I6V2I0 |
| B | DNA (27-mer) | dna | 27 | — | — |
| C | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.69 | 0.97 | 15 | empty |
| 2 | 776 | 0.67 | 0.75 | 52 | empty |
| 3 | 395 | 0.66 | 0.80 | 36 | empty |
| 4 | 58 | 0.40 | 0.81 | 19 | empty |
| 5 | 111 | 0.39 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1189 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- A–C · 761 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 572 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7K32 · Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with an abasic… · 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 I6V2I0
- Elsewhere: RCSB PDB 7K32 · PDBe 7K32 · UniProt I6V2I0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.