MolNFT v2 · #216961 · protein + RNA
MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
8PPL · Eukaryotic translation initiation factor 3 subunit K: “MERS-CoV Nsp1 bound to the human 43S pre-initiation complex”. Electron microscopy at 2.65, 5 ligands (GTP, MET, MG), 20 pockets (best druggability 0.88). MolNFT v2 #216961 on…
- PDB
- 8PPL
- Type
- protein + RNA
- Length
- 11,624 residues
- Chains
- 52
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Homo sapiens; Middle East respiratory syndrome-related coronavirus
- Molecule
- Eukaryotic translation initiation factor 3 subunit K; Eukaryotic translation initiation…
- EC
- 3.4.19.12, 3.6.5.3, 4.2.99.18
- UniProt
- Q9UBQ5, O00303, Q9Y262, Q7L2H7, O15372, O75821, P41567, P47813, P05198, P20042, P41091, Q14152, P60228, O15371, Q99613, P08865, P61247, P15880, P23396, P62701, P46782, P62753, P62081, P62241, P46781, P46783, P62280, P25398, P62277, P62263, P62841, P62249, P08708, P62269, P39019, P60866, P63220, P62244, A0A4W2DI10, P62847, P62851, P62854, P42677, P62857, P62273, P62861, P62979, P63244, P62945, K9N7C7
- Ligands
- GTP, MET, MG, ZN, UNX
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 2.65 · 52 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I3 | Eukaryotic translation initiation factor 3 subunit K | protein | 217 | 59% helix, 1% strand | Q9UBQ5 |
| I4 | Eukaryotic translation initiation factor 3 subunit F (EC 3.4.19.12) | protein | 268 | 48% helix, 22% strand | O00303 |
| I5 | Eukaryotic translation initiation factor 3 subunit L | protein | 372 | 64% helix, 1% strand | Q9Y262 |
| I6 | Eukaryotic translation initiation factor 3 subunit M | protein | 345 | 68% helix, 4% strand | Q7L2H7 |
| I8 | Eukaryotic translation initiation factor 3 subunit H | protein | 318 | 55% helix, 16% strand | O15372 |
| Io | Eukaryotic translation initiation factor 3 subunit G | protein | 77 | 25% helix, 34% strand | O75821 |
| Ip | Eukaryotic translation initiation factor 1 | protein | 105 | 22% helix, 32% strand | P41567 |
| Iq | Eukaryotic translation initiation factor 1A, X-chromosomal | protein | 103 | 9% helix, 36% strand | P47813 |
| Ir | Eukaryotic translation initiation factor 2 subunit 1 | protein | 293 | 43% helix, 21% strand | P05198 |
| Is | Eukaryotic translation initiation factor 2 subunit 2 | protein | 159 | 35% helix, 21% strand | P20042 |
| It | Eukaryotic translation initiation factor 2 subunit 3 (EC 3.6.5.3) | protein | 451 | 18% helix, 39% strand | P41091 |
| Iu | Eukaryotic translation initiation factor 3 subunit A | protein | 587 | 72% helix, 3% strand | Q14152 |
| Iv | Eukaryotic translation initiation factor 3 subunit E | protein | 430 | 75% helix, 2% strand | P60228 |
| Iw | Met-tRNAi(Met) | rna | 75 | — | — |
| Ix | Eukaryotic translation initiation factor 3 subunit D | protein | 455 | 23% helix, 25% strand | O15371 |
| Iy | Eukaryotic translation initiation factor 3 subunit C | protein | 633 | 68% helix, 3% strand | Q99613 |
| A2 | 18S rRNA | rna | 1780 | — | — |
| AA | 40S ribosomal protein SA | protein | 216 | 43% helix, 14% strand | P08865 |
| AB | 40S ribosomal protein S3a | protein | 224 | 28% helix, 33% strand | P61247 |
| AC | 40S ribosomal protein S2 | protein | 218 | 34% helix, 27% strand | P15880 |
| AD | 40S ribosomal protein S3 (EC 4.2.99.18) | protein | 225 | 35% helix, 27% strand | P23396 |
| AE | 40S ribosomal protein S4, X isoform | protein | 262 | 19% helix, 30% strand | P62701 |
| AF | 40S ribosomal protein S5 | protein | 192 | 51% helix, 8% strand | P46782 |
| AG | 40S ribosomal protein S6 | protein | 240 | 33% helix, 22% strand | P62753 |
| AH | 40S ribosomal protein S7 | protein | 188 | 38% helix, 24% strand | P62081 |
| AI | 40S ribosomal protein S8 | protein | 205 | 34% helix, 25% strand | P62241 |
| AJ | 40S ribosomal protein S9 | protein | 180 | 53% helix, 6% strand | P46781 |
| AK | 40S ribosomal protein S10 | protein | 97 | 39% helix, 16% strand | P46783 |
| AL | 40S ribosomal protein S11 | protein | 151 | 7% helix, 32% strand | P62280 |
| AM | 40S ribosomal protein S12 | protein | 123 | 48% helix, 15% strand | P25398 |
| AN | 40S ribosomal protein S13 | protein | 149 | 58% helix, 0% strand | P62277 |
| AO | 40S ribosomal protein S14 | protein | 135 | 25% helix, 25% strand | P62263 |
| AP | 40S ribosomal protein S15 | protein | 131 | 36% helix, 15% strand | P62841 |
| AQ | 40S ribosomal protein S16 | protein | 142 | 43% helix, 22% strand | P62249 |
| AR | 40S ribosomal protein S17 | protein | 134 | 47% helix, 6% strand | P08708 |
| AS | Small ribosomal subunit protein uS13 | protein | 145 | 44% helix, 9% strand | P62269 |
| AT | Small ribosomal subunit protein eS19 | protein | 144 | 53% helix, 14% strand | P39019 |
| AU | 40S ribosomal protein S20 | protein | 101 | 25% helix, 47% strand | P60866 |
| AV | 40S ribosomal protein S21 | protein | 83 | 20% helix, 27% strand | P63220 |
| AW | 40S ribosomal protein S15a | protein | 129 | 34% helix, 31% strand | P62244 |
| AX | 40S ribosomal protein S23 | protein | 141 | 26% helix, 29% strand | A0A4W2DI10 |
| AY | 40S ribosomal protein S24 | protein | 124 | 36% helix, 29% strand | P62847 |
| AZ | 40S ribosomal protein S25 | protein | 72 | 47% helix, 21% strand | P62851 |
| Aa | 40S ribosomal protein S26 | protein | 101 | 19% helix, 23% strand | P62854 |
| Ab | 40S ribosomal protein S27 | protein | 83 | 11% helix, 24% strand | P42677 |
| Ac | 40S ribosomal protein S28 | protein | 65 | 0% helix, 45% strand | P62857 |
| Ad | 40S ribosomal protein S29 | protein | 55 | 36% helix, 9% strand | P62273 |
| Ae | Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein | protein | 59 | 31% helix, 0% strand | P62861 |
| Af | Ubiquitin-40S ribosomal protein S27a | protein | 74 | 7% helix, 22% strand | P62979 |
| Ag | Receptor of activated protein C kinase 1 | protein | 314 | 0% helix, 53% strand | P63244 |
| Ah | 60S ribosomal protein L41 | protein | 25 | 76% helix, 0% strand | P62945 |
| Aj | Host translation inhibitor nsp1 | protein | 29 | 69% helix, 0% strand | K9N7C7 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains Is, It
- MET · Methionine · ligand · chains It, Iw
- MG · Magnesium ion · metal · 116 copies · chains It, A2, AE, Aa, AO, AB, AI, AL, AT, AN, Aj, AQ, AF, AG, AS, AX
- ZN · Zinc ion · metal · 4 copies · chains Is, Aa, Ad, Af
- UNX · Unknown atom or ion · ion · 129 copies · chains Iw, A2, AB, Aa, AL, AQ, AX, AI, AN, AE, AT, AC, AF, AZ, AS, AJ, AO, Ad
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 | 1171 | 0.88 | 0.90 | 115 | MG, UNX |
| 2 | 1152 | 0.88 | 0.90 | 90 | UNX, MG |
| 3 | 729 | 0.87 | 0.91 | 77 | empty |
| 4 | 1117 | 0.86 | 0.88 | 95 | UNX |
| 5 | 849 | 0.86 | 0.89 | 85 | MG, UNX |
Interfaces
156 interfaces between chains.
- A2–AG · 5869 Ų buried · 149 hydrogen bonds · protein-nucleic
- I4–I8 · 4527 Ų buried · 41 hydrogen bonds · protein-protein
- A2–AI · 4353 Ų buried · 103 hydrogen bonds · protein-nucleic
- A2–AE · 4069 Ų buried · 75 hydrogen bonds · protein-nucleic
- A2–AJ · 3716 Ų buried · 80 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 100 modified, 1 covalent (nucleotide modification, nonstandard, acetylation, covalent ligand).
Compared structures
- P41091 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain It against A, TM-score 1.00
- P62263 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S14 (P62263) · a predicted model of the same protein · chain AO against A, TM-score 0.99
- O00303 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain I4 against A, TM-score 0.97
- P62241 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S8 (P62241) · a predicted model of the same protein · chain AI against A, TM-score 0.96
- P25398 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S12 (P25398) · a predicted model of the same protein · chain AM against A, TM-score 0.96
- O75821 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain Io against A, TM-score 0.95
- P62269 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S18 (P62269) · a predicted model of the same protein · chain AS against A, TM-score 0.94
- O15372 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain I8 against A, TM-score 0.94
- P62273 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S29 (P62273) · a predicted model of the same protein · chain Ad against A, TM-score 0.93
- Q14152 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain Iu against A, TM-score 0.92
- P60228 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain Iv against A, TM-score 0.92
- Q99613 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain Iy against A, TM-score 0.90
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 Q9UBQ5
- Every structure of UniProt O00303
- Every structure of UniProt Q9Y262
- Every structure of UniProt Q7L2H7
- Every structure of UniProt O15372
- Every structure of UniProt O75821
- Every structure of UniProt P41567
- Every structure of UniProt P47813
- Every structure of UniProt P05198
- Every structure of UniProt P20042
- Every structure of UniProt P41091
- Every structure of UniProt Q14152
- Every structure of UniProt P60228
- Every structure of UniProt O15371
- Every structure of UniProt Q99613
- 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 A0A4W2DI10
- 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 P62979
- Every structure of UniProt P63244
- Every structure of UniProt P62945
- Every structure of UniProt K9N7C7
- Elsewhere: RCSB PDB 8PPL · PDBe 8PPL · UniProt Q9UBQ5 · UniProt O00303 · UniProt Q9Y262 · UniProt Q7L2H7 · UniProt O15372 · UniProt O75821 · UniProt P41567 · UniProt P47813 · UniProt P05198 · UniProt P20042 · UniProt P41091 · UniProt Q14152 · UniProt P60228 · UniProt O15371 · UniProt Q99613 · 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 A0A4W2DI10 · UniProt P62847 · UniProt P62851 · UniProt P62854 · UniProt P42677 · UniProt P62857 · UniProt P62273 · UniProt P62861 · UniProt P62979 · UniProt P63244 · UniProt P62945 · UniProt K9N7C7
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