MolNFT v1 · #159741 · protein + RNA
Crystal structure of mus musculus (mm) endonuclease V in complex with a 23MER RNA oligo containing an inosine after a 180 min soak in 10 mm MN2+
6OZP: “Crystal structure of mus musculus (mm) endonuclease V in complex with a 23MER RNA oligo containing an inosine…”. X-ray diffraction, 1 ligand (MN), 3 pockets (best druggability 0.86). MolNFT v1 #159741 on GenesisL1: 3D structure…
- PDB
- 6OZP
- Type
- protein + RNA
- Length
- 520 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V; DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)- 3'); RNA…
- EC
- 3.1.26.-
- UniProt
- Q8C9A2
- Ligands
- MN
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease V (EC 3.1.26.-) | protein | 244 | 34% helix, 24% strand | Q8C9A2 |
| B | Endonuclease V (EC 3.1.26.-) | protein | 244 | 34% helix, 23% strand | Q8C9A2 |
| c, d | DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)- 3') | rna | 4 | — | — |
| C, D | RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3') | rna | 12 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 11 copies · chains A, C, c, B, D, d
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
- PG4 · Tetraethylene 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.86 | 0.88 | 50 | MN |
| 2 | 114 | 0.42 | 0.77 | 18 | empty |
| 3 | 52 | 0.24 | 0.73 | 12 | empty |
Interfaces
11 interfaces between chains.
- A–c · 614 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–d · 604 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 559 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- B–C · 428 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 417 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6OZP · Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo… · the same entry in another collection · chain D against D, 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 6OZP · PDBe 6OZP · UniProt Q8C9A2
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