MolNFT v1 · #102069 · protein + RNA
Complete human RNase L in complex with 2-5A (5'-ppp heptamer), amppcp and RNA substrate.
4OAV · Protein (RNase L): “Complete human RNase L in complex with 2-5A (5'-ppp heptamer), amppcp and RNA substrate.”. X-ray diffraction, 4 ligands (ACP, PUP, MG), 16 pockets (best druggability 0.77). MolNFT v1 #102069 on GenesisL1: 3D…
- PDB
- 4OAV
- Type
- protein + RNA
- Length
- 1,355 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (RNase L); RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')
- UniProt
- Q05823
- Ligands
- ACP, PUP, MG, PO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Protein (RNase L) | protein | 673 | 49% helix, 8% strand | Q05823 |
| A, C | RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2') | rna | 4 | — | — |
| D | Protein (RNase L) | protein | 674 | 49% helix, 8% strand | Q05823 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains B, D
- PUP · (2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate · ligand · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains B, D
- PO4 · Phosphate ion · ion · 6 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.77 | 0.80 | 81 | PO4 |
| 2 | 1164 | 0.76 | 0.78 | 117 | PO4 |
| 3 | 778 | 0.74 | 0.79 | 76 | empty |
| 4 | 251 | 0.66 | 0.83 | 36 | ACP |
| 5 | 536 | 0.65 | 0.77 | 46 | empty |
Interfaces
5 interfaces between chains.
- B–D · 3460 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 622 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 616 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–C · 415 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–A · 344 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4OAV · Complete human RNase L in complex with 2-5A (5'-ppp heptamer), AMPPCP and RNA substrate. · the same entry in another collection · chain B against B, TM-score 1.00
- Q05823 · AlphaFold monomer V2.0 prediction for 2-5A-dependent ribonuclease (Q05823) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q05823
- Elsewhere: RCSB PDB 4OAV · PDBe 4OAV · UniProt Q05823
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