MolNFT v1 · #159737 · protein + RNA
Crystal structure of mus musculus (mm) endonuclease V in complex with a 23MER RNA oligo containing an inosine after a 2 min soak in MN2+
6OZL: “Crystal structure of mus musculus (mm) endonuclease V in complex with a 23MER RNA oligo containing an inosine…”. X-ray diffraction, 2 ligands (MN, NA), 2 pockets (best druggability 0.80). MolNFT v1 #159737 on GenesisL1: 3D…
- PDB
- 6OZL
- Type
- protein + RNA
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V; DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)…
- EC
- 3.1.26.-
- UniProt
- Q8C9A2
- Ligands
- MN, NA
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease V (EC 3.1.26.-) | protein | 243 | 35% helix, 24% strand | Q8C9A2 |
| B | Endonuclease V (EC 3.1.26.-) | protein | 244 | 34% helix, 24% strand | Q8C9A2 |
| C | DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)- R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3') | rna | 15 | — | — |
| D | DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)- R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3') | rna | 16 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.80 | 0.88 | 31 | GOL |
| 2 | 475 | 0.80 | 0.88 | 28 | TLA |
Interfaces
5 interfaces between chains.
- A–C · 789 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 781 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 580 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–C · 455 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 360 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6OZL · Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8C9A2 · AlphaFold monomer V2.0 prediction for endonuclease V (Q8C9A2) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q8C9A2
- Elsewhere: RCSB PDB 6OZL · PDBe 6OZL · UniProt Q8C9A2
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