MolNFT v1 · #172023 · protein + RNA
SARS-cov-2-NSP1-40S complex, focused on head
6ZOL · 18S ribosomal RNA: “SARS-cov-2-NSP1-40S complex, focused on head”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #172023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZOL
- Type
- protein + RNA
- Length
- 2,416 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 18S ribosomal RNA; 40S ribosomal protein S3; 40S ribosomal protein S5; 40S ribosomal…
- EC
- 4.2.99.18
- UniProt
- P23396, P46782, P46783, P25398, P62841, P62249, P08708, P62269, P39019, P60866, P62851, P62857, P62273, Q5RKT7, P63244
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 16 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 18S ribosomal RNA | rna | 472 | — | — |
| D | 40S ribosomal protein S3 (EC 4.2.99.18) | protein | 225 | 37% helix, 28% strand | P23396 |
| F | 40S ribosomal protein S5 | protein | 190 | 53% helix, 9% strand | P46782 |
| K | 40S ribosomal protein S10 | protein | 97 | 42% helix, 16% strand | P46783 |
| M | 40S ribosomal protein S12 | protein | 123 | 44% helix, 16% strand | P25398 |
| P | 40S ribosomal protein S15 | protein | 124 | 37% helix, 15% strand | P62841 |
| Q | 40S ribosomal protein S16 | protein | 142 | 43% helix, 20% strand | P62249 |
| R | 40S ribosomal protein S17 | protein | 81 | 67% helix, 2% strand | P08708 |
| S | 40S ribosomal protein S18 | protein | 143 | 45% helix, 9% strand | P62269 |
| T | 40S ribosomal protein S19 | protein | 144 | 53% helix, 14% strand | P39019 |
| U | 40S ribosomal protein S20 | protein | 101 | 27% helix, 47% strand | P60866 |
| Z | 40S ribosomal protein S25 | protein | 72 | 47% helix, 21% strand | P62851 |
| c | 40S ribosomal protein S28 | protein | 61 | 0% helix, 49% strand | P62857 |
| d | 40S ribosomal protein S29 | protein | 55 | 38% helix, 11% strand | P62273 |
| f | Ribosomal protein S27A | protein | 72 | 4% helix, 22% strand | Q5RKT7 |
| g | Receptor of activated protein C kinase 1 | protein | 314 | 1% helix, 53% strand | P63244 |
Ligands and binding sites
- MG · Magnesium ion · metal · 57 copies · chains 2, S, T, Q, Z, f, F
- ZN · Zinc ion · metal · 2 copies · chains d, f
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.88 | 0.91 | 88 | MG |
| 2 | 846 | 0.87 | 0.90 | 80 | MG |
| 3 | 812 | 0.86 | 0.90 | 83 | MG |
| 4 | 1062 | 0.86 | 0.88 | 83 | empty |
| 5 | 761 | 0.85 | 0.90 | 73 | MG |
Interfaces
34 interfaces between chains.
- 2–T · 3051 Ų buried · 59 hydrogen bonds · protein-nucleic
- 2–Q · 2970 Ų buried · 57 hydrogen bonds · protein-nucleic
- 2–S · 2333 Ų buried · 55 hydrogen bonds · protein-nucleic
- 2–d · 2153 Ų buried · 34 hydrogen bonds · protein-nucleic
- 2–P · 2071 Ų buried · 51 hydrogen bonds · protein-nucleic
Compared structures
- 6ZOL · SARS-CoV-2-Nsp1-40S complex, focused on head · the same entry in another collection · chain U against U, 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 P23396
- Every structure of UniProt P46782
- Every structure of UniProt P46783
- Every structure of UniProt P25398
- Every structure of UniProt P62841
- Every structure of UniProt P62249
- Every structure of UniProt P08708
- Every structure of UniProt P62269
- Every structure of UniProt P39019
- Every structure of UniProt P60866
- Every structure of UniProt P62851
- Every structure of UniProt P62857
- Every structure of UniProt P62273
- Every structure of UniProt Q5RKT7
- Every structure of UniProt P63244
- Elsewhere: RCSB PDB 6ZOL · PDBe 6ZOL · UniProt P23396 · UniProt P46782 · UniProt P46783 · UniProt P25398 · UniProt P62841 · UniProt P62249 · UniProt P08708 · UniProt P62269 · UniProt P39019 · UniProt P60866 · UniProt P62851 · UniProt P62857 · UniProt P62273 · UniProt Q5RKT7 · UniProt P63244
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