Table 1.
Models of SARS‐CoV‐2 protein a .
| Gene | Protein | Name | Length | Model template | Model | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PDB ID | Identity (%) | Coverage (%) | Model description | Region | Interacting protein | Ligand | Rotamer outlier (%) | Ramachandran outlier (%) | Clash score | ||||
| orf1ab | YP_009725297.1 | Leader protein | 180 | 2HSXA | 85.3 | 66.7 | monomer(A) | A: 10–129 | 0.97 | 0 | 4.75 | ||
| YP_009725298.1 | nsp2 | 638 | n.a. | ||||||||||
| YP_009725299.1 | Papain‐like proteinase (nsp3) | 1945 | 2IDYA | 79.3 | 5.9 | monomer(A) | A: 1–114 | 0.98 | 0 | 4.55 | |||
| 2FAVC | 72.5 | 9.2 | monomer(A) | A: 202–379 | 0.67 | 0 | 4.41 | ||||||
| 2WCTB | 76.3 | 13.9 | homo‐dimer(A, B) | A, B: 410–679 | 1.27 | 0 | 4.96 | ||||||
| 2KQWA | 72.7 | 3.7 | monomer(A) | A: 675–746 | 1.52 | 0 | 4.41 | ||||||
| 5E6JA | 82.0 | 16.6 | monomer(A) | A: 745–1067 | 0.35 | 0 | 3.71 | ||||||
| 2K87A | 81.0 | 6.3 | monomer(A) | A: 1085–1206 | 1.79 | 0 | 3.58 | ||||||
| YP_009725300.1 | nsp4 | 500 | 3GZFA | 40.0 | 20.4 | homo‐dimer(A, B) | A: 399–500 B: 399–497 | 1.69 | 0 | 3.43 | |||
| YP_009725301.1 | 3C‐like proteinase | 306 | 6LU7A | 100.0 | 100.0 | homo‐dimer(A, C) | A, C: 1–306 | AZP, Carfilzomib | 0 | 0 | 4.54 | ||
| YP_009725302.1 | nsp6 | 290 | n.a. | ||||||||||
| YP_009725303.1 | nsp7 | 83 | 2KYSA | 98.8 | 100.0 | monomer(A) | A: 1–83 | 1.3 | 0 | 4.57 | |||
| YP_009725304.1 | nsp8 | 198 | 2AHMH | 97.4 | 98.5 | hetero‐16mer(E, F, G, H, S, T, U, V) | E, S: 35–195 F, T: 47–195 G, U: 1–194 H, V: 1–195 | nsp7 (A, B, C, D, O, P, Q, R) | 1.08 | 0 | 4.42 | ||
| YP_009725305.1 | nsp9 | 113 | 1UW7A | 97.3 | 100.0 | homo‐dimer(A, B) | A, B: 1–113 | 1.6 | 0 | 4.86 | |||
| YP_009725306.1 | nsp10 | 139 | 5NFYH | 98.5 | 96.4 | hetero‐dimer(B) | B: 1–134 | 3'‐to‐5' exonuclease (A) | ZN | 1.23 | 0 | 4.78 | |
| YP_009725307.1 | RNA‐dependent RNA polymerase | 932 | 6NURA | 96.3 | 86.8 | hetero‐tetramer(A) | A: 114–922 | nsp8 (B, D), nsp7(C) | ZN | 0.81 | 0 | 4.87 | |
| YP_009725308.1 | Helicase | 601 | 5WWPA | 71.5 | 99.7 | monomer(A) | A: 1–599 | ZN | 1.54 | 0 | 4.82 | ||
| YP_009725309.1 | 3'‐to‐5' Exonuclease | 527 | 5NFYD | 94.7 | 100.0 | hetero‐dimer(A) | A: 1–527 | nsp10 (B) | ZN | 1.23 | 0 | 4.78 | |
| YP_009725310.1 | Endo‐RNAse | 346 | 2H85A | 88.1 | 100.0 | homo‐hexamer(A, B, C, D, E, F) | A, B, C, D, E, F: 1–346 | 0.92 | 0 | 4.75 | |||
| YP_009725311.1 | 2'‐O‐Ribose methyltransferase | 298 | 5YNIA | 66.3 | 100.0 | hetero‐dimer(A) | A: 1–298 | nsp10 (B) | GTG, ZN, Sinefungin | 1.66 | 0 | 4.69 | |
| GTG, ZN, Tecadenoson | 1.66 | 0 | 4.55 | ||||||||||
| GTG, ZN, Selodenoson | 1.39 | 0 | 4.55 | ||||||||||
| GTG, ZN, Trabodenoson | 1.39 | 0 | 4.40 | ||||||||||
| YP_009725312.1 | nsp11 | 13 | n.a. | ||||||||||
| S | YP_009724390.1 | Surface glycoprotein | 1273 | 6VSBA | 100.0 | 88.6 | homo‐trimer(A, B, C) | A, B, C: 13–1140 | ACE2 (D) | EAL | 1.75 | 0.08 | 5.58 |
| LPR | 1.72 | 0.08 | 5.58 | ||||||||||
| X8Z | 1.72 | 0.08 | 5.60 | ||||||||||
| ORF3a | YP_009724391.1 | ORF3a protein | 275 | n.a. | |||||||||
| E | YP_009724392.1 | Envelope protein | 75 | 5X29E | 91.4 | 90.7 | homo‐pentamer(A, B, C, D, E) | A, C, D, E: 5–68 B: 1–68 | 1.67 | 0 | 4.63 | ||
| M | YP_009724393.1 | Membrane glycoprotein | 222 | n.a. | |||||||||
| ORF6 | YP_009724394.1 | ORF6 protein | 61 | n.a. | |||||||||
| ORF7a | YP_009724395.1 | ORF7a protein | 121 | 1YO4A | 88.4 | 75.2 | monomer(A) | A: 11–101 | 0 | 0 | 4.92 | ||
| ORF7b | YP_009725296.1 | ORF7b | 43 | n.a. | |||||||||
| ORF8 | YP_009724396.1 | ORF8 protein | 121 | n.a. | |||||||||
| N | YP_009724397.2 | Nucleocapsid phosphoprotein | 419 | 1SSKA | 81.6 | 39.1 | monomer(A) | A: 20–183 | 1.56 | 0 | 4.88 | ||
| 2JW8B | 95.8 | 30.1 | homo‐dimer(A, B) | A: 243–367 B: 242–367 | 0.48 | 0 | 3.31 | ||||||
| ORF10 | YP_009725255.1 | ORF10 protein | 38 | n.a. | |||||||||
a
‘Protein’ indicates RefSeq IDs of SARS‐CoV‐2 proteins and also serves as the model identifiers. ‘Model template’: ‘Identity’ and ‘Coverage’ show amino acid sequence identity and coverage of the template structure (‘PDB ID’) to the corresponding SARS‐CoV‐2 proteins. ‘Model’: ‘Model description’ and ‘Interacting protein’ show chain ID(s) of the corresponding and bounding proteins, respectively. ‘Region’ shows chain ID(s) and the start and end residue numbers of modeled region. ‘Ligand’ shows the names or PDB codes of ligands in the template or model structures. ‘Rotamer outlier’, ‘Ramachandran outlier’, and ‘Clash score’ show the parameters of the models.