MolNFT v1 · #157657 · protein + RNA
Vibrio cholerae oligoribonuclease bound to pag
6N6D: “Vibrio cholerae oligoribonuclease bound to pag”. X-ray diffraction, 1 ligand (NA), 2 pockets (best druggability 0.42). MolNFT v1 #157657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N6D
- Type
- protein + RNA
- Length
- 183 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligoribonuclease; RNA (5'-R(P*AP*G)-3')
- EC
- 3.1.-.-
- UniProt
- A0A0H6V4D7
- Ligands
- NA
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligoribonuclease (EC 3.1.-.-) | protein | 181 | 45% helix, 18% strand | A0A0H6V4D7 |
| D | RNA (5'-R(P*AP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.42 | 0.80 | 17 | empty |
| 2 | 72 | 0.32 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–D · 472 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6N6D · Vibrio cholerae Oligoribonuclease bound to pAG · 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 A0A0H6V4D7
- Elsewhere: RCSB PDB 6N6D · PDBe 6N6D · UniProt A0A0H6V4D7
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