SARS-CoV-2 Protein Homology Models

Models of the SARS-CoV-2 proteins – downloadable in PDB format on this page – were constructed using the AS2TS software package. 

Protein sequences come from the SARS-CoV-2 reference genome here and here.  Names and annotations in the following table come from that source.

The last part of each PDB file name indicates the model template by PDB ID and chain.  For example, the nsp1 model is based on template PDB 2gdt, chain A.  Each file includes additional information in REMARK fields.

Name

Long name

Annotation

Protein

Length

Coverage

Homology models

nsp1

leader protein

  

YP_009725297.1

 18013-127 2gdt_A    

nsp2

    

YP_009725298.1

 638      

nsp3

  

conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP);

YP_009725299.1

 19451-111 207-373 413-676 746-1064 1089-1203 6w9c_A 5e6j_A 5tl7_B 2w2g_A 6w02_B 2k87_A 2gri_A

nsp4

nsp4B_TM

contains transmembrane domain 2 (TM2);

YP_009725300.1

 500403-499 3vcb_A 3gzf_A  

nsp5

3C-like proteinase

nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003);

YP_009725301.1

 3061-306 5r82_A 6lu7_A 3tnt_A

nsp6

nsp6_TM

putative transmembrane domain

YP_009725302.1

 290      

nsp7

    

YP_009725303.1

 831-83 6m71_C 5f22_A 3ub0_B

nsp8

    

YP_009725304.1

 1981-191 2ahm_G    

nsp9

  

ssRNA-binding protein;

YP_009725305.1

 1131-113 6w9q_A 6w4b_B 1uw7_A

nsp10

nsp10_CysHis

formerly known as growth-factor-like protein (GFL);

YP_009725306.1

 1391-131 5c8t_A 5nfy_N  
             

nsp12

RNA-dependent RNA polymerase

NiRAN and RdRp

YP_009725307.1

 9321-932 6m71_A 7btf_A 6nur_A

nsp13

helicase

nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding domain (ZD), NTPase/helicase domain (HEL), RNA 5'-triphosphatase

YP_009725308.1

 6011-596 6jyt_A 5wwp_B  

nsp14

3'-to-5' exonuclease"

nsp14A2_ExoN and nsp14B_NMT;

YP_009725309.1

 5271-525 5c8s_B 5c8t_B  

nsp15

endoRNAse

nsp15-A1 and nsp15B-NendoU;

YP_009725310.1

 3461-345 6w01_A 2h85_A  

nsp16

2'-O-ribose methyltransferase

nsp16_OMT; 2'-o-MT;

YP_009725311.1

 2981-298 6w4h_A 6w61_A  

S

spike

surface glycoprotein

YP_009724390.1

 127318-1147 6vsb_C 6vxx_B 6acc_A 6m0j_E 6lzg_B 6w41_C

ORF3a

ORF3a protein

  

YP_009724391.1

 275      

E

envelope protein

ORF4; structural protein; E protein

YP_009724392.1

 75 5x29_A 2mm4_A  

M

membrane glycoprotein

ORF5; structural protein

YP_009724393.1

 222      

ORF6

ORF6 protein

  

YP_009724394.1

 61      

ORF7a

ORF7a protein

  

YP_009724395.1

 12115-98 1xak_A 1yo4_A  

ORF7b

    

YP_009725318.1

 43      

ORF8

ORF8 protein

  

YP_009724396.1

 121      

N

nucleocapsid phosphoprotein

ORF9; structural protein

YP_009724397.2

 41947-173 250-364 6yi3_A 6m3m_B 6vyo_D 2cjr_A

ORF10

ORF10 protein

  

YP_009725255.1

 38      

Models/methods: Molecular docking | Single-point GBSA | “Fusion” machine learning model | MD-trajectory-average GBSA | Safety and pharmacokinetic property predictions