MolNFT v1 · #85130 · protein + RNA
Structure of duck rig-I C-terminal domain (ctd) with 14-mer dsrna
4A2X · Retinoic acid inducible protein I: “Structure of duck rig-I C-terminal domain (ctd) with 14-mer dsrna”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.66). MolNFT v1 #85130 on GenesisL1: 3D structure, binding sites…
- PDB
- 4A2X
- Type
- protein + RNA
- Length
- 536 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid inducible protein I; 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3'…
- UniProt
- D3TI84
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Retinoic acid inducible protein I | protein | 120 | 20% helix, 43% strand | D3TI84 |
| L, N | 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3' | rna | 14 | — | — |
| M, O | 5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3' | rna | 14 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.66 | 0.77 | 35 | empty |
| 2 | 602 | 0.62 | 0.74 | 32 | empty |
| 3 | 353 | 0.59 | 0.77 | 26 | empty |
| 4 | 495 | 0.58 | 0.74 | 30 | empty |
| 5 | 76 | 0.48 | 0.83 | 14 | empty |
Interfaces
15 interfaces between chains.
- L–M · 668 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- N–O · 666 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–L · 316 Ų buried · 2 hydrogen bonds · protein-nucleic
- D–N · 303 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–O · 294 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 4A2X · Structure of duck RIG-I C-terminal domain (CTD) with 14-mer dSRNA · 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 D3TI84
- Elsewhere: RCSB PDB 4A2X · PDBe 4A2X · UniProt D3TI84
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