Research workbench
Structure of E. COLI exoix in complex with the palindromic 5OV6 oligonucleotide and potassium
Analyse Structure of E. COLI exoix in complex with the palindromic 5OV6 oligonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZDD
- Type
- protein + DNA
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein xni; 5OV6 DNA
- EC
- 3.1.-.-
- UniProt
- Q8X6R9
- Ligands
- K
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein xni (EC 3.1.-.-) | protein | 247 | 54% helix, 12% strand | Q8X6R9 |
| B | 5OV6 DNA | dna | 10 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · chains A, B
- IPA · Isopropyl alcohol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.68 | 0.77 | 65 | empty |
Interfaces
1 interface between chains.
- A–B · 257 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 3ZDD · Structure of E. coli ExoIX in complex with the palindromic 5ov6 oligonucleotide and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X6R9 · AlphaFold monomer V2.0 prediction for flap endonuclease xni (Q8X6R9) · 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 Q8X6R9
- Elsewhere: RCSB PDB 3ZDD · PDBe 3ZDD · UniProt Q8X6R9
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