MolNFT v1 · #106353 · protein + RNA
Crystal structure of the pre-reactive state of porcine OAS1
4RWN · 2'-5'-oligoadenylate synthase 1: “Crystal structure of the pre-reactive state of porcine OAS1”. X-ray diffraction, 2 ligands (APC, MG), 4 pockets (best druggability 0.72). MolNFT v1 #106353 on GenesisL1: 3D structure, binding sites…
- PDB
- 4RWN
- Type
- protein + RNA
- Length
- 387 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-5'-oligoadenylate synthase 1; RNA (5'- R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*…
- EC
- 2.7.7.84
- UniProt
- Q29599
- Ligands
- APC, MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-5'-oligoadenylate synthase 1 (EC 2.7.7.84) | protein | 349 | 49% helix, 11% strand | Q29599 |
| B | RNA (5'- R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*UP*GP*AP*A)-3') | rna | 19 | — | — |
| C | RNA (5'- R(*UP*UP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3') | rna | 19 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 4 copies · chains A, B
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 | 996 | 0.72 | 0.76 | 47 | MG |
| 2 | 729 | 0.68 | 0.76 | 59 | APC, MG |
| 3 | 60 | 0.32 | 0.76 | 13 | empty |
| 4 | 51 | 0.28 | 0.75 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–C · 923 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 877 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- A–B · 752 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4RWN · Crystal structure of the pre-reactive state of porcine OAS1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q29599 · AlphaFold monomer V2.0 prediction for 2'-5'-oligoadenylate synthase 1 (Q29599) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q29599
- Elsewhere: RCSB PDB 4RWN · PDBe 4RWN · UniProt Q29599
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