P0DTC1 | SWISS-MODEL Repository

P0DTC1 (R1A_SARS2) Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

Replicase polyprotein 1a UniProtKB InterPro Interactive Modelling

4405 aa; Sequence (Fasta) ; 2 identical sequences: Severe acute respiratory syndrome coronavirus 2: A0A6G7KRG6, A0A6G6A224

It is possible new templates exist for this target since these models were created.

Available Structures

Host translation inhibitor nsp1 1-180; PRO_0000449635

Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
7k7p.1.A	monomer	0.76	10-126	100.00
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6zoj.1.8	monomer	0.67	148-180	100.00
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Non-structural protein 2 181-818; PRO_0000449636

	Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
	7msw.1.A	monomer	0.84	184-818	3×ZN;	100.00
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Papain-like protease nsp3 819-2763; PRO_0000449637

Description	PDB ID	Oligo-state	Range	Seq id (%)	Ligands
Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an…	8cx9 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	Heteromer P62987;	1565-1878	100	1×ZN; 2×BR;
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Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant	7d6h PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	1563-1878	99.68	2×ZN; 2×PO4;
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Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, meth…	7ofu PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	1564-1878	100	2×HE9; 4×GOL; 2×ZN; 8×PO4; 2×CL;
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SARS-CoV-2 PLpro in complex with inhibitor WEHI-P24	9cyk PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	1565-1872	99.66	2×A1A0V; 2×ACY; 2×GOL;
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Structure of SARS-CoV-2 NSP3 macrodomain in the apo form	8azc PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	1024-1192	100	2×CL; 2×MPO;
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SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89	7lbr PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1564-1878	100	1×ZN; 2×SO4; 1×XT7; 1×GOL;
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SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83	7llf PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1564-1878	100	1×ZN; 4×SO4; 2×BO3; 1×Y54;
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SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-24	7lbs PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1564-1878	100	1×XR8; 1×ZN; 2×SO4; 3×BO3;
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Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors	8z4w PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1565-1877	100	1×A1D7X; 1×ZN;
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SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472	9csy PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1566-1878	99.68	1×A1AZ1; 1×TFA; 1×ZN;
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SARS CoV-2 PLpro in complex with inhibitor 3k	7tzj PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1566-1875	99.67	1×S88; 4×ZN; 1×DMS;
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SARS-CoV-2 PLpro in complex with inhibitor WEHI-P4	9cyd PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1570-1878	99.68	1×A1A0U; 2×ZN; 1×CL;
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SARS-CoV-2 PLpro in complex with inhibitor WEHI-P1	9cyb PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1565-1872	99.66	1×A1A0T; 1×SIN;
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SARS-CoV-2 PLpro in complex with inhibitor WEHI-P2	9cyc PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	1565-1871	99.66	1×A1A0S; 1×ACY; 3×GOL;
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Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
6ywk.3.A	monomer	0.84	1025-1194		100.00
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6w9c.1.A	monomer	0.80	1566-1878	1×ZN;	100.00
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3e9s.1.A	monomer	0.79	1564-1877	1×TTT; 1×ZN;	82.86
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7cmd.4.A	monomer	0.79	1564-1878	1×TTT; 1×ZN;	100.00
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2w2g.1.A	monomer	0.79	1231-1494		75.00
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6wuu.2.A	monomer	0.79	1562-1879	1×ACE; 1×ZN;	99.69
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2kqv.1.A	monomer	0.75	1369-1493		78.13
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2kqw.1.A	monomer	0.71	1496-1550		80.22
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2k87.1.A	monomer	0.69	1907-2021		81.74
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Non-structural protein 4 2764-3263; PRO_0000449638

	Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
	3vcb.1.A	homo-2-mer	0.72	3174-3262		61.36
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3C-like proteinase nsp5 3264-3569; PRO_0000449639

Description	PDB ID	Oligo-state	Range	Seq id (%)	Ligands
Structure of compound 1 bound to SARS-CoV-2 main protease	9hjh PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100.0	2×A1IVK; 4×EDO; 3×BR; 1×NA;
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Structure of compound 119 bound to SARS-CoV-2 main protease	9hak PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×A1ITI; 1×CL; 1×NA;
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Structure of compound 1 bound to SARS-CoV-2 main protease	9haj PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×A1ITJ; 1×DMS; 1×CL;
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CRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE COMPLEXED WITH FRAGMENT F01	7p51 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	4×NA; 4×DMS; 2×5P9;
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SARS-CoV-2 Mpro (Omicron, P132H+T169S) in complex with alpha-ketoamide 13b-K	8r1q PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	99.35	2×O6K;
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Crystal structure of SARS-CoV-2 Mpro in complex with cyclic peptide GM4 including unnatural amino a…	7z4s PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×PEG; 1×DMS; 2×EDO; 1×PGE;
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SARS-CoV-2 Main protease bound to a non-covalent non-peptidic HTS hit	8w1t PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	4×DMS; 3×EDO; 1×SO4; 2×A1A21; 2×A1AFD; 1×GOL;
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SARS-CoV-2 Mpro (Omicron, P132H+T169S) free enzyme	8r24 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	99.35
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Crystal structure of SARS-CoV-2 Mpro with compound 12	9gil PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×A1IL7; 7×SO4; 5×GOL; 2×EDO;
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SARS-CoV2 Main Protease (Mpro) in complex with the covalent inhibitor 28a	9gf7 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×A1IYL;
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Structure of SARS-CoV-2 Mpro in complex with its degrader	8yls PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×A1LYZ;
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Crystal structure of SARS-CoV-2 Mpro with AB-343.	9glv PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×A1IMY; 1×CL; 2×PEG; 2×EDO;
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T21I Mutant	8tyk PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	99.67
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Crystal structure of the Mpro of SARS COV-2 in complex with the MG-87 inhibitor	9gmq PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100	2×MXU; 1×CL;
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F/E166A/L167F Triple Mutant	8u25 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	99.02
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Crystal structure of SARS-CoV-2 Main Protease (Mpro) with covalent inhibitor 5,8-Dihydroxy-1,4-naph…	8ws3 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3569	100.0	2×PEG; 1×X7F; 1×DMS;
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SARS-CoV-2 Mpro in complex with a silicon-containing inhibitor	9h0f PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3568	100	1×GOL; 2×A1IRW; 14×SO4; 9×CL; 1×DMS;
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Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Nirmatrelvir	9bo4 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3568	99.67	2×4WI;
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SARS-CoV-2 Mpro (Omicron,P132H) in complex with alpha-ketoamide 13b-K at pH 8.5	8r26 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3568	99.67	2×O6K; 1×CL;
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Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 44	8y44 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3567	100	2×A1D50;
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SARS-COV2 Main Protease in complex with inhibitor MG-131	7z0p PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3567	100	2×I8H; 2×NA;
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SARS-CoV-2 Mpro in Complex with RK-107	8aj1 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3567	100	2×A1IMU;
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Crystal structure of SARS-CoV-2 Mpro with compound 5	9gij PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3566	100	2×A1IL0;
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Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with X77	8ykn PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3265-3567	99.67	2×X77;
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Crystal Structure of T21I SARS-CoV-2 Main Protease	9bnt PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3566	99.67
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Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Compound Mpro61	9bo0 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3566	99.67	1×XEK;
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Crystal structure of the SARS-CoV-2 main protease in complex with SY110	8hhu PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3566	99.67	2×LVX;
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Crystal structure of SARS-Cov-2 main protease E166N mutant in complex with Bofutrelvir	8ywy PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3567	99.34	2×FHR;
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Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 51	8y42 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3565	100	2×A1D51;
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SARS-CoV-2 3CL protease (3CL pro) in complex with a novel inhibitor	8z46 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3564	100	2×A1D70;
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SARS-COV2 Main Protease in complex with inhibitor MG78	7ql8 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3564	100	2×I70; 2×CL; 4×NA;
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SARS-CoV-2 Mpro in complex with compound 12d inhibitor	9bbp PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3564	100	2×GLY; 2×VAL; 2×THR; 2×PHE; 2×A1ALW;
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Crystal structure of the SARS-CoV-2 main protease in complex with Hit-1	8hht PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3564	100.0	2×LV0; 4×DMS;
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Crystal structure of SARS-Cov-2 main protease in complex with X77	8ykj PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3566	100	2×X77;
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Crystal structure of SARS-CoV-2 main protease in complex with C5	8y7u PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3564	99.67	2×A1LX2;
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Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with X77	8ykp PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3566	99.67	2×X77;
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Crystal structure of SARS-CoV-2 main protease in complex with C2	8y7t PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3564	99.67	2×A1LX1;
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Crystal structure of SARS-CoV-2 main protease in complex with TMP1	9izb PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3564	100
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Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with GC376	9bo8 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3264-3563	99.67	2×UED;
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Crystal structure of SARS-Cov-2 main protease, pH=6.5	8wsj PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3564	100
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Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with X77	8ykq PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3564	99.67	2×X77;
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Crystal structure of SARS-Cov-2 main protease in complex with S217622	8hur PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3563	100	2×7YY;
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Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with X77	8ykm PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3563	99.66	2×X77;
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Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4	9lvt PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3563	100.0	2×A1L7Q;
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Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with PF07321332	7xb4 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3563	99.66	2×4WI;
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Crystal structure of SARS-Cov-2 main protease, pH=6.0	8wsi PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3563	100.0
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Crystal structure of SARS-Cov-2 main protease, pH=8.5	8wsk PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3561	100.0
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Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with shikonin	8wur PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3266-3561	99.32	1×FNO;
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Crystal structure of SARS main protease in complex with PF-00835231	8z1h PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3267-3562	96.19	2×V2M;
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Crystal structure of SARS-Cov-2 main protease D48N mutant	7xb3 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	homo-2-mer	3267-3561	99.66
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SARS-CoV-2 3CLpro bound to covalent inhibitor	8wz0 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	3264-3568	100	1×XQF;
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Crystal structure of SARS-CoV-2 3CL protease in complex with compound 17 (S-892216)	9lvv PDBe PDBe-KB PDBj PDBsum RCSB SMTL	monomer	3266-3564	100	1×A1L7R;
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Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
5rfv.1.B	homo-2-mer	0.91	3264-3567	2×T8J;	100.00
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5r7z.1.B	homo-2-mer	0.91	3264-3567	2×HWH;	100.00
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2z9j.1.A	homo-2-mer	0.89	3264-3567	2×DTZ;	96.08
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6lu7.1.B	homo-2-mer	0.89	3264-3569		100.00
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6y2g.1.A	homo-2-mer	0.88	3264-3566	1×GLY; 2×O6K;	100.00
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2a5i.1.B	homo-2-mer	0.87	3264-3569	2×AZP;	96.08
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Non-structural protein 7 3860-3942; PRO_0000449641

Description	PDB ID	Oligo-state	Range	Seq id (%)	Ligands
SARS-CoV-2 core polymerase complex inhibited by araCTP	9blf PDBe PDBe-KB PDBj PDBsum RCSB SMTL	Heteromer P0DTD1;	3860-3932	100	2×ZN; 2×MG; 2×HF4;
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Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mecha…	7eiz PDBe PDBe-KB PDBj PDBsum RCSB SMTL	Heteromer P0DTD1;	3861-3932	100	13×ZN; 1×MG;
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SARS-CoV-2 C-RTC with 13-TP	9l09 PDBe PDBe-KB PDBj PDBsum RCSB SMTL	Heteromer P0DTD1;	3861-3932	100	2×ZN; 2×MG;
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SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-cap…	8xch PDBe PDBe-KB PDBj PDBsum RCSB SMTL	Heteromer P0DTD1;	3861-3932	100	32×ZN; 2×ADP; 2×MG; 1×PO4;
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Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
6m71.1.B	monomer	0.80	3861-3930	100.00
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7jlt.1.A	monomer	0.79	3860-3938	100.00
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2ahm.1.B	monomer	0.75	3860-3933	98.80
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Non-structural protein 8 3943-4140; PRO_0000449642

Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
2ahm.1.H	monomer	0.77	3944-4134	97.47
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7jlt.1.D	monomer	0.76	4019-4135	100.00
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6nur.1.B	monomer	0.76	4019-4133	97.47
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2ahm.1.E	monomer	0.70	3980-4134	97.47
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6m71.1.D	monomer	0.70	4020-4133	100.00
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RNA-capping enzyme subunit nsp9 4141-4253; PRO_0000449643

Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
1qz8.1.A	homo-2-mer	0.79	4143-4253	97.35
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6w4b.1.A	homo-2-mer	0.79	4141-4253	100.00
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1uw7.1.B	homo-2-mer	0.73	4141-4253	97.35
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Non-structural protein 10 4254-4392; PRO_0000449644

Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
2g9t.1.A	homo-12-mer	0.80	4261-4382	24×ZN;	97.12
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6w4h.1.B	monomer	0.77	4271-4386	2×ZN;	100.00
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	Model ID	Oligo-state	Avg pLDDT	Range	Trg-Mdl Seq Id (%)

	Model ID	Oligo-state	Avg Confidence	Range	Trg-Mdl Seq id (%)