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SARS-CoV-2 protein components. Summary and comments of PDB entries
Protein component	Function	PDB ID and link	Resolution method	Ligand
Nsp1	It suppresses host gene expression by ribosome association. It blocks the innate immune responses that would otherwise facilitate clearance of the infection	6ZLW	Electron Microscopy	human 40S ribosomal subunit
		6ZM7	Electron Microscopy	human CCDC124-80S-EBP1 ribosome complex
		6ZME	Electron Microscopy	human CCDC124-80S-eERF1 ribosome complex
		6ZMI	Electron Microscopy	human LYAR-80S ribosome complex
		6ZMT	Electron Microscopy	pre-40S-like ribosome complex
		6ZN5	Electron Microscopy	pre-40S-like ribosome complex - state 2
		6ZP4	Electron Microscopy	human 43S preinitiation ribosome complex - state 2
Nsp2	Nsp2, along with nsp1, are involved in suppressing gene expression	-
Nsp3	Involved in viral replication. The Nsp3-4-6 complex regulates the replication site by recruiting the replicase proteins to the host membrane. Nsp3, Nsp4 and Nsp6 assemble at the endoplasmic reticulum, driving its modification and formation of the DMV (double membrane vesicles) Papain-like protease domain	6W6Y	X-Ray Diffraction	AMP (ADENOSINE MONOPHOSPHATE)
		6WUU	X-Ray Diffraction	peptide inhibitor VIR250
		6W9C	X-Ray Diffraction
		6VXS	X-Ray Diffraction
		6W02	X-Ray Diffraction	ADP ribose
		6WCF	X-Ray Diffraction	MES, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
		6WEN	X-Ray Diffraction
		6WEY	X-Ray Diffraction
		6WRH	X-Ray Diffraction
		6WX4	X-Ray Diffraction	peptide inhibitor VIR251
		6WZU	X-Ray Diffraction	P3221 space group
		6XAA	X-Ray Diffraction	ubiquitin propargylamide
		6XA9	X-Ray Diffraction	SG15 C-terminal domain propargylamide
		6XG3	X-Ray Diffraction
		6YWK	X-Ray Diffraction	HEPES
		6YWL	X-Ray Diffraction	ADP-ribose
		6YWM	X-Ray Diffraction	MES, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Nsp4	Nsp3-4-6 complex for endoplasmic reticulum modification and formation of DMVs	-
Nsp5	Main protease	6LU7	X-Ray Diffraction	inhibitor N3
		6LZE	X-Ray Diffraction	inhibitor 11a
		6M03	X-Ray Diffraction
		6M0K	X-Ray Diffraction	inhibitor 11b
		6M2N	X-Ray Diffraction	novel inhibitor
		6M2Q
		6W63	X-Ray Diffraction	non-covalent inhibitor X77
		6WTT	X-Ray Diffraction	inhibitor GC-376
		6XCH	X-Ray Diffraction	Leupeptin
		6WQF	X-Ray Diffraction
		6XKH	X-Ray Diffraction	Oxidized C145 (sulfinic acid cysteine)
		6Y2G	X-Ray Diffraction	α-ketoamide inhibitor.
		6Y2E	X-Ray Diffraction
		6Y2F	X-Ray Diffraction	α-ketoamide inhibitor.
		6Y84	X-Ray Diffraction
		6YB7	X-Ray Diffraction
		6YNQ	X-Ray Diffraction	2-Methyl-1-tetralone
		6YVA	X-Ray Diffraction	mISG15
		6YVF	X-Ray Diffraction	AZD6482
		6Z2E	X-Ray Diffraction	biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone
		6WNP	X-Ray Diffraction	Boceprevir
		6WTK	X-Ray Diffraction	Feline coronavirus drug
		6WTM	X-Ray Diffraction	Feline coronavirus drug
		6WTJ	X-Ray Diffraction	Feline coronavirus drug
		6XA4	X-Ray Diffraction	UAW241
		6XB0	X-Ray Diffraction
		6XB1	X-Ray Diffraction
		6XB2	X-Ray Diffraction
		6XBG	X-Ray Diffraction	UAW246
		6XBH	X-Ray Diffraction	UAW247
		6XBI	X-Ray Diffraction	UAW248
		6XHM	X-Ray Diffraction	Ketone-Based Covalent Inhibitors
		6XHU	X-Ray Diffraction
		6XFN	X-Ray Diffraction	UAW243
		6XKF	X-Ray Diffraction	oxidized Cys145
		6XMK	X-Ray Diffraction	inhibitor 7j
		6YZ6	X-Ray Diffraction	Leupeptin
		7B83	X-Ray Diffraction	pyrithione zinc
		7BRP	X-Ray Diffraction	Boceprevir
		7BQY	X-Ray Diffraction	Inhibitor N3
		7BUY	X-Ray Diffraction	carmofur
		7C8R	X-Ray Diffraction	TG-0203770
		7C8T	X-Ray Diffraction	TG-0205221
		7C8U	X-Ray Diffraction	GC376
		7D1M	X-Ray Diffraction	GC376
Nsp6	Nsp3-4-6 complex for endoplasmic reticulum modification and formation of DMVs	-
Nsp7-Nsp8-Nsp12 Complex (RNA-dependent RNA polymerase) (RdRp)	Part of the replication-transcription complex, involved in virus replication	6M5I	Electron Microscopy	nsp7-nsp8c complex
		6M71	Electron Microscopy
		6WIQ	Electron Microscopy	nsp7-nsp8c complex
		6WQD	Electron Microscopy	nsp7-nsp8c complex
		6WTC	Electron Microscopy	nsp7-nsp8c complex
		6XEZ	Electron Microscopy	nsp7, nsp8, nsp12 bound to nsp13
		6XIP	Electron Microscopy	nsp7-nsp8c complex
		6XQB	Electron Microscopy	nsp7-nsp8c complex
		6YHU	Electron Microscopy	nsp7-nsp8c complex
		6YYT	Electron Microscopy
		7AAP	Electron Microscopy	primer dsRNA and favipiravir-RTP
		7BTF	Electron Microscopy
		7BV1	Electron Microscopy
		7BV2	Electron Microscopy	template-primer RNA and triphosphate form of Remdesivir(RTP)
		7BW4	Electron Microscopy
		7BZF	Electron Microscopy	nsp7-nsp8c complex
		7C2K	Electron Microscopy	nsp7-nsp8c complex
Nsp9	RNA replicase	6W9Q	X-Ray Diffraction
		6W4B	X-Ray Diffraction
		6WXD	X-Ray Diffraction
Nsp10-Nsp16	Nsp10 plays multiple roles in RNA capping	6XKM	X-Ray Diffraction	nsp16-nsp10 with SAM (S-ADENOSYLMETHIONINE)
		6W4H	X-Ray Diffraction	nsp16-nsp10 complex
		6W61	X-Ray Diffraction	nsp16-nsp10 complex
		6W75	X-Ray Diffraction	nsp16-nsp10 complex
		6WJT	X-Ray Diffraction	nsp16-nsp10 with S-Adenosyl-L-Homocysteine
		6WQ3	X-Ray Diffraction	nsp16-nsp10 7-methyl-GpppA and S-adenosyl-L-homocysteine
		6WKS	X-Ray Diffraction	nsp16-nsp10 with RNA cap analogue (m7GpppA) and S-adenosylmethionine
		6WKQ	X-Ray Diffraction	nsp10-nsp16 with Sinefungin
		6WRZ	X-Ray Diffraction	nsp16-nsp10 with 7-methyl-GpppA, S-adenosyl-L-homocysteine and Sulfates
		6WVN	X-Ray Diffraction	nsp16-nsp10 with 7-methyl-GpppA and S-Adenosylmethionine
		6YZ1	X-Ray Diffraction	nsp10-nsp16 with Sinefungin
		6ZCT	X-Ray Diffraction	nsp10
		7BQ7	X-Ray Diffraction	nsp16-nsp10 complex
		7C2I	X-Ray Diffraction	nsp16-nsp10 with SAM
		7C2J	X-Ray Diffraction	nsp16-nsp10 with SAM
Nsp11		-
Nsp13		6XEZ	Electron Microscopy	nsp7, nsp8, nsp12 bound to nsp13
Nsp14		-
Nsp15	RNA endonuclease	6VWW	X-Ray Diffraction
		6W01	X-Ray Diffraction	Citrate
		6WLC	X-Ray Diffraction	Uridine-5'-Monophosphate
		6WXC	X-Ray Diffraction	Tipiracil
		6X1B	X-Ray Diffraction	Nucleotide GpU
		6XDH	X-Ray Diffraction
S	Spike (S) glycoprotein	6LVN	X-Ray Diffraction	S2 subunit
		6LZG	X-Ray Diffraction	Receptor Binding Domain (RBD) of S with ACE2
		6LXT	X-Ray Diffraction	S2 subunit
		6M0J	X-Ray Diffraction	RBD with ACE2
		6M17	Electron Microscopy	RBD with ACE2-B0AT1 complex
		6M1V	X-Ray Diffraction	S2 subunit
		6ZER	X-Ray Diffraction	RBD with EY6A Fab
		6ZGH	Electron Microscopy
		6ZGG	Electron Microscopy
		6VSB	Electron Microscopy
		6VW1	X-Ray Diffraction	RBD with ACE2
		6VXX	Electron Microscopy
		6VYB	Electron Microscopy
		6W41	X-Ray Diffraction	RBD with CR3022
		6WPS	Electron Microscopy	S309 neutralizing antibody Fab fragment
		6WPT	Electron Microscopy	S309 neutralizing antibody Fab fragment
		6X29	Electron Microscopy
		6X2A	Electron Microscopy
		6X2B	Electron Microscopy
		6X2C	Electron Microscopy
		6X6P	Electron Microscopy
		6XC2	X-Ray Diffraction	RBD with antibody CC12.1
		6XC3	X-Ray Diffraction	RBD with antibodies CC12.1 and CR3022
		6XC4	X-Ray Diffraction	RBD with antibody CC12.3
		6XCM	Electron Microscopy	C105 neutralizing antibody Fab fragment (state 1)
		6XCN	Electron Microscopy	C105 neutralizing antibody Fab fragment (state 2)
		6XDG	Electron Microscopy	RBD with the Fab fragments of two neutralizing antibodies
		6XE1	X-Ray Diffraction	RBD with CV30 Fab
		6XKL	Electron Microscopy
		6XR8	Electron Microscopy
		6XRA	Electron Microscopy
		6YLA	X-Ray Diffraction	RBD with CR3022 Fab
		6YMO	X-Ray Diffraction	RBD with CR3022 Fab
		6YOR	Electron Microscopy	S1 unit with CR3022 Fab
		6YZ5	X-Ray Diffraction	RBD with nanobody H11-D4
		6ZGE	Electron Microscopy
		6ZGI	Electron Microscopy
		7BWJ	X-Ray Diffraction	RBD with an antibody
		7BYR	Electron Microscopy	BD23-Fab
		7C01	X-Ray Diffraction	RBD with CB6 antibody
		7C2L	Electron Microscopy	4A8
		7DDD	Electron Microscopy
		7DDN	Electron Microscopy
		7JWB	Electron Microscopy	Trimerized VH binder
		7T9J	Electron Microscopy	SARS-CoV-2 Omicron spike protein
		7T9L	Electron Microscopy	SARS-CoV-2 Omicron spike protein in complex with human ACE2
Orf3a	Increased formation of DMVs	6XDC	Electron Microscopy
		7KJR	Electron Microscopy	Apolipoprotein A-I
Orf3b	Downregulates IFN-I ( Human type I interferons) signaling	-
Orf6	Interferon antagonist	-
Orf7a	Favors apoptotic activity of infected cells	6W37	Diffraction
Orf7b	Favors apoptotic activity of infected cells	-
Orf8	Interferes with immune responses	7JTL	X-Ray Diffraction
		7JX6	X-Ray Diffraction
Orf9b	Interferon antagonist	2CME	X-Ray Diffraction
		6Z4U	X-Ray Diffraction
		7KDT	Electron Microscopy	Human mitochondrial receptor Tom70
Orf9c		-
Orf10		-
E	Envelope (E) protein, involved in virus packaging	7K3G	Solid-State NMR
M	Membrane (M) protein, involved in virus packaging	-
N	Nucleocapsid (N) protein, involved in RNA binding and packaging	6M3M	X-Ray Diffraction
		6VYO	X-Ray Diffraction
		6WKP	X-Ray Diffraction	monoclinic crystal form
		6WJI	X-Ray Diffraction
		6WZO	X-Ray Diffraction
		6WZQ	X-Ray Diffraction
		6YI3	NMR
		6YUN	X-Ray Diffraction
		6ZCO	X-Ray Diffraction
		7ACS	NMR	7mer dsRNA
		7ACT	NMR	10mer ssRNA
		7C22	X-Ray Diffraction
		7CE0	X-Ray Diffraction
		7CDZ	X-Ray Diffraction
		7DE1	X-Ray Diffraction
Results of the project “Prediction of the structure of SARS-CoV-2 proteins with artificial intelligence techniques”, funded by Axencia Galega de Innovación (GAIN) and co-funded by FEDER, and supported by Consellería de Economía, Emprego e Industria, reference: IN845D-02. Resultados do proxecto “Predición da estrutura de proteínas de SARS-CoV-2 con técnicas de intelixencia artificial”, subvencionado pola Axencia Galega de Innovación (GAIN) e cofinanciado con cargo aos fondos FEDER, e apoiado pola Consellería de Economía, Emprego e Industria, referencia: IN845D-02.