Research workbench
Structure of E. COLI exoix in complex with a fragment of the FLAP1 DNA oligonucleotide, potassium and magnesium
Analyse Structure of E. COLI exoix in complex with a fragment of the FLAP1 DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZDA
- Type
- protein + DNA
- Length
- 257 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein xni; 5'-D(*GP*CP*GP*CP)-3'; 5'-D(*AP*AP*GP*CP*GP*CP)-3'
- EC
- 3.1.-.-
- UniProt
- Q8X6R9
- Ligands
- PIV, K, MG, PO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein xni (EC 3.1.-.-) | protein | 247 | 54% helix, 13% strand | Q8X6R9 |
| B | 5'-D(*GP*CP*GP*CP)-3' | dna | 4 | — | — |
| C | 5'-D(*AP*AP*GP*CP*GP*CP)-3' | dna | 6 | — | — |
Ligands and binding sites
- PIV · Pivalic acid · ligand · chains A
- K · Potassium ion · metal · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.73 | 0.77 | 73 | MG |
| 2 | 53 | 0.39 | 0.80 | 12 | PO4 |
Interfaces
3 interfaces between chains.
- B–C · 216 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- A–B · 162 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3ZDA · Structure of E. coli ExoIX in complex with a fragment of the Flap1 DNA oligonucleotide… · 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 3ZDA · PDBe 3ZDA · UniProt Q8X6R9
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