MolNFT v1 · #191343 · protein + RNA
Gramp non-match pfs target RNA
8D8N · Ramp superfamily protein: “Gramp non-match pfs target RNA”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #191343 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8D8N
- Type
- protein + RNA
- Length
- 1,312 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ramp superfamily protein; RNA (35-mer); RNA (5'…
- UniProt
- A0A0B0EGF3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ramp superfamily protein | protein | 1256 | 26% helix, 20% strand | A0A0B0EGF3 |
| C | RNA (35-mer) | rna | 35 | — | — |
| D | RNA (5'- R(P*UP*CP*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*A)- 3') | rna | 21 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.82 | 0.89 | 52 | empty |
| 2 | 118 | 0.78 | 0.97 | 24 | empty |
| 3 | 545 | 0.77 | 0.85 | 46 | empty |
| 4 | 409 | 0.72 | 0.83 | 47 | empty |
| 5 | 660 | 0.71 | 0.78 | 47 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5966 Ų buried · 122 hydrogen bonds · protein-nucleic
- B–D · 1605 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 756 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 8D8N · gRAMP non-match PFS target RNA · 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 A0A0B0EGF3
- Elsewhere: RCSB PDB 8D8N · PDBe 8D8N · UniProt A0A0B0EGF3
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