MolNFT v1 · #103788 · protein + RNA
A second look at the hdv ribozyme structure and dynamics.
4PR6 · Hdv ribozyme self-cleaved: “A second look at the hdv ribozyme structure and dynamics.”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.68). MolNFT v1 #103788 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4PR6
- Type
- protein + RNA
- Length
- 167 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hdv ribozyme self-cleaved; U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hdv ribozyme self-cleaved | rna | 72 | — | — |
| A | U1 small nuclear ribonucleoprotein a | protein | 95 | 32% helix, 25% strand | P09012 |
Ligands and binding sites
- MG · Magnesium ion · metal · 16 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.68 | 0.82 | 33 | empty |
| 2 | 462 | 0.60 | 0.76 | 26 | empty |
| 3 | 109 | 0.41 | 0.77 | 20 | empty |
| 4 | 67 | 0.25 | 0.72 | 10 | MG |
Interfaces
1 interface between chains.
- B–A · 973 Ų buried · 33 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4PR6 · A Second Look at the HDV Ribozyme Structure and Dynamics. · the same entry in another collection · chain B against B, 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 P09012
- Elsewhere: RCSB PDB 4PR6 · PDBe 4PR6 · UniProt P09012
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