MolNFT v1 · #172021 · protein + RNA
SARS-cov-2-NSP1-40S complex, composite MAP
6ZOJ · 18S ribosomal RNA: “SARS-cov-2-NSP1-40S complex, composite MAP”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #172021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZOJ
- Type
- protein + RNA
- Length
- 6,618 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 18S ribosomal RNA; 40S ribosomal protein sa; 40S ribosomal protein S3A; 40S ribosomal…
- EC
- 4.2.99.18, 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P08865, P61247, P15880, P23396, P62701, P46782, P62753, P62081, P62241, P46781, P46783, P62280, P25398, P62277, P62263, P62841, P62249, P08708, P62269, P39019, P60866, P63220, P62244, P62266, P62847, P62851, P62854, P42677, P62857, P62273, P62861, Q5RKT7, P63244, P0DTD1, P62945
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 36 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 18S ribosomal RNA | rna | 1704 | — | — |
| A | 40S ribosomal protein sa | protein | 216 | 39% helix, 14% strand | P08865 |
| B | 40S ribosomal protein S3A | protein | 213 | 29% helix, 35% strand | P61247 |
| C | 40S ribosomal protein S2 | protein | 218 | 33% helix, 27% strand | P15880 |
| D | 40S ribosomal protein S3 (EC 4.2.99.18) | protein | 225 | 37% helix, 28% strand | P23396 |
| E | 40S ribosomal protein S4, X isoform | protein | 262 | 18% helix, 32% strand | P62701 |
| F | 40S ribosomal protein S5 | protein | 190 | 54% helix, 9% strand | P46782 |
| G | 40S ribosomal protein S6 | protein | 230 | 28% helix, 24% strand | P62753 |
| H | 40S ribosomal protein S7 | protein | 186 | 41% helix, 23% strand | P62081 |
| I | 40S ribosomal protein S8 | protein | 205 | 31% helix, 25% strand | P62241 |
| J | 40S ribosomal protein S9 | protein | 180 | 53% helix, 6% strand | P46781 |
| K | 40S ribosomal protein S10 | protein | 97 | 41% helix, 16% strand | P46783 |
| L | 40S ribosomal protein S11 | protein | 151 | 7% helix, 32% strand | P62280 |
| M | 40S ribosomal protein S12 | protein | 123 | 44% helix, 17% strand | P25398 |
| N | 40S ribosomal protein S13 | protein | 149 | 58% helix, 0% strand | P62277 |
| O | 40S ribosomal protein S14 | protein | 135 | 26% helix, 25% strand | P62263 |
| 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 | 132 | 48% helix, 6% 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 |
| V | 40S ribosomal protein S21 | protein | 83 | 19% helix, 27% strand | P63220 |
| W | 40S ribosomal protein S15A | protein | 129 | 32% helix, 27% strand | P62244 |
| X | 40S ribosomal protein S23 | protein | 141 | 26% helix, 29% strand | P62266 |
| Y | 40S ribosomal protein S24 | protein | 124 | 35% helix, 29% strand | P62847 |
| Z | 40S ribosomal protein S25 | protein | 72 | 47% helix, 21% strand | P62851 |
| a | 40S ribosomal protein S26 | protein | 101 | 16% helix, 23% strand | P62854 |
| b | 40S ribosomal protein S27 | protein | 82 | 7% helix, 29% strand | P42677 |
| c | 40S ribosomal protein S28 | protein | 61 | 0% helix, 49% strand | P62857 |
| d | 40S ribosomal protein S29 | protein | 55 | 38% helix, 11% strand | P62273 |
| e | 40S ribosomal protein S30 | protein | 56 | 23% helix, 0% strand | P62861 |
| 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 |
| j | Non-structural protein 1 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 33 | 64% helix, 0% strand | P0DTD1 |
| h | 60S ribosomal protein L41 | protein | 25 | 72% helix, 0% strand | P62945 |
Ligands and binding sites
- MG · Magnesium ion · metal · 166 copies · chains 2, S, T, F, Q, Z, f, a, h, j, N, E, C, L, X, I, G, O
- ZN · Zinc ion · metal · 3 copies · chains a, 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 | 1103 | 0.89 | 0.92 | 129 | MG |
| 2 | 1139 | 0.88 | 0.90 | 116 | MG |
| 3 | 834 | 0.88 | 0.91 | 88 | MG |
| 4 | 802 | 0.87 | 0.90 | 93 | MG |
| 5 | 838 | 0.87 | 0.90 | 72 | empty |
Interfaces
94 interfaces between chains.
- 2–G · 5128 Ų buried · 112 hydrogen bonds · protein-nucleic
- 2–I · 4239 Ų buried · 87 hydrogen bonds · protein-nucleic
- 2–E · 3717 Ų buried · 64 hydrogen bonds · protein-nucleic
- 2–J · 3574 Ų buried · 73 hydrogen bonds · protein-nucleic
- 2–X · 3304 Ų buried · 77 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ZOJ · SARS-CoV-2-Nsp1-40S complex, composite map · the same entry in another collection · chain E against E, 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 P08865
- Every structure of UniProt P61247
- Every structure of UniProt P15880
- Every structure of UniProt P23396
- Every structure of UniProt P62701
- Every structure of UniProt P46782
- Every structure of UniProt P62753
- Every structure of UniProt P62081
- Every structure of UniProt P62241
- Every structure of UniProt P46781
- Every structure of UniProt P46783
- Every structure of UniProt P62280
- Every structure of UniProt P25398
- Every structure of UniProt P62277
- Every structure of UniProt P62263
- 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 P63220
- Every structure of UniProt P62244
- Every structure of UniProt P62266
- Every structure of UniProt P62847
- Every structure of UniProt P62851
- Every structure of UniProt P62854
- Every structure of UniProt P42677
- Every structure of UniProt P62857
- Every structure of UniProt P62273
- Every structure of UniProt P62861
- Every structure of UniProt Q5RKT7
- Every structure of UniProt P63244
- Every structure of UniProt P0DTD1
- Every structure of UniProt P62945
- Elsewhere: RCSB PDB 6ZOJ · PDBe 6ZOJ · UniProt P08865 · UniProt P61247 · UniProt P15880 · UniProt P23396 · UniProt P62701 · UniProt P46782 · UniProt P62753 · UniProt P62081 · UniProt P62241 · UniProt P46781 · UniProt P46783 · UniProt P62280 · UniProt P25398 · UniProt P62277 · UniProt P62263 · UniProt P62841 · UniProt P62249 · UniProt P08708 · UniProt P62269 · UniProt P39019 · UniProt P60866 · UniProt P63220 · UniProt P62244 · UniProt P62266 · UniProt P62847 · UniProt P62851 · UniProt P62854 · UniProt P42677 · UniProt P62857 · UniProt P62273 · UniProt P62861 · UniProt Q5RKT7 · UniProt P63244 · UniProt P0DTD1 · UniProt P62945
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