MolNFT v1 · #84203 · protein + DNA
Structure of E. COLI exoix in complex with the palindromic 5OV6 oligonucleotide and potassium
3ZDD · Protein xni: “Structure of E. COLI exoix in complex with the palindromic 5OV6 oligonucleotide and potassium”. X-ray diffraction, 1 ligand (K), 1 pocket (best druggability 0.68). MolNFT v1 #84203 on GenesisL1: 3D structure, binding…
- 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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