MolNFT v1 · #159734 · protein + DNA
Crystal structure of ciona intestinalis (ci) endonuclease V (D234N) in complex with a 23MER DNA containing an inosine followed by a ribo- adenosine
6OZI · Endonuclease V isoform X2: “Crystal structure of ciona intestinalis (ci) endonuclease V (D234N) in complex with a 23MER DNA containing an…”. X-ray diffraction, 1 ligand (K), 3 pockets (best druggability 0.85). MolNFT v1 #159734 on…
- PDB
- 6OZI
- Type
- protein + DNA
- Length
- 522 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V isoform X2; DNA/RNA (23-mer)
- UniProt
- A0A3Q0JV13
- Ligands
- K
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease V isoform X2 | protein | 244 | 39% helix, 25% strand | A0A3Q0JV13 |
| B | Endonuclease V isoform X2 | protein | 241 | 38% helix, 25% strand | A0A3Q0JV13 |
| C | DNA/RNA (23-mer) | dna | 17 | — | — |
| D | DNA/RNA (23-mer) | dna | 20 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.85 | 0.86 | 61 | K |
| 2 | 343 | 0.72 | 0.85 | 41 | empty |
| 3 | 78 | 0.34 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 911 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–D · 872 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 740 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–D · 599 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 313 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6OZI · Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a… · 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 A0A3Q0JV13
- Elsewhere: RCSB PDB 6OZI · PDBe 6OZI · UniProt A0A3Q0JV13
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