MolNFT v1 · #159733 · protein + DNA
Crystal structure of ciona intestinalis (ci) endonuclease V in complex with a 24MER DNA containing an inosine followed by a ribo-adenosine
6OZH · Endonuclease V isoform X2: “Crystal structure of ciona intestinalis (ci) endonuclease V in complex with a 24MER DNA containing an inosine…”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.83). MolNFT v1 #159733 on…
- PDB
- 6OZH
- Type
- protein + DNA
- Length
- 1,042 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V isoform X2; DNA/RNA (5'-D(P*CP*GP*GP*TP*AP*AP*CP*CP*GP*I)-R(P*A)…
- UniProt
- A0A3Q0JV13
- Ligands
- CA
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endonuclease V isoform X2 | protein | 241 | 37% helix, 26% strand | A0A3Q0JV13 |
| C | Endonuclease V isoform X2 | protein | 239 | 38% helix, 26% strand | A0A3Q0JV13 |
| D | Endonuclease V isoform X2 | protein | 239 | 38% helix, 26% strand | A0A3Q0JV13 |
| E, F | DNA/RNA (5'-D(P*CP*GP*GP*TP*AP*AP*CP*CP*GP*I)-R(P*A)- D(P*TP*AP*TP*GP*CP*AP*GP*CP*AP*TP*TP*TP*C)-3') | dna | 19 | — | — |
| G, H | DNA/RNA (5'-D(P*CP*GP*GP*TP*AP*AP*CP*CP*GP*I)-R(P*A)- D(P*TP*AP*TP*GP*CP*AP*GP*CP*AP*TP*TP*TP*C)-3') | dna | 22 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.83 | 0.86 | 61 | empty |
| 2 | 814 | 0.83 | 0.86 | 57 | empty |
| 3 | 113 | 0.46 | 0.79 | 19 | empty |
| 4 | 95 | 0.44 | 0.79 | 19 | empty |
| 5 | 93 | 0.43 | 0.79 | 17 | empty |
Interfaces
15 interfaces between chains.
- C–G · 916 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–H · 878 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–F · 870 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–E · 859 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–G · 570 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 6OZH · Crystal structure of Ciona intestinalis (Ci) Endonuclease V in complex with a 24mer DNA… · 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 6OZH · PDBe 6OZH · UniProt A0A3Q0JV13
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