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: A0A6G6A224, A0A6G7KRG6

Available Structures

Host translation inhibitor nsp1 1-180; PRO_0000449635

Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
7k7p.1.A	monomer	0.81	10-126	100.00
Assess
6zoj.1.8	monomer	0.67	148-180	100.00
Assess

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
Assess

Papain-like protease nsp3 819-2763; PRO_0000449637

Description	PDB ID	Oligo-state	Range	Ligands
The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a …	7uv5 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	Heteromer P0CG47; P0CG48;	1567-1878	1×ZN; 4×EDO;
Assess
Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant	7d6h SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1563-1878	1×ZN; 1×PO4;
Assess
Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, meth…	7ofu SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×HE9; 2×GOL; 1×ZN; 4×PO4; 1×CL;
Assess
Structure of SARS-CoV-2 Papain-like Protease bound to N-(2-pyrrolidyl)-3,4,5-trihydroxybenzoylhydra…	7qcg SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×DZI; 2×GOL; 1×ZN; 1×CL; 4×PO4;
Assess
Structure of SARS-CoV-2 Papain-like Protease bound to N-(3,4-dihydroxybenzylidene)-thiosemicarbazone	7qci SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×A6Q; 2×GOL; 1×ZN; 5×PO4; 1×CL;
Assess
Structure of SARS-CoV-2 Papain-like Protease bound to N-(3-methoxy-4-hydroxy-acetophenone)thiosemic…	7qcm SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×A3X; 5×GOL; 1×ZN; 3×CL; 3×PO4;
Assess
Structure of SARS-CoV-2 Papain-like Protease bound to N-(2,4-dihydroxybenzylidene)-thiosemicarbazone	7qcj SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	5×GOL; 1×A4O; 1×ZN; 3×PO4; 5×CL;
Assess
Structure of SARS-CoV-2 Papain-like Protease bound to N-(3,5-dimethoxy-4-hydroxybenzyliden)thiosemi…	7qch SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×A5I; 2×GOL; 1×ZN; 5×PO4; 1×CL;
Assess
Structure of SARS-CoV-2 Papain-like Protease bound to N-(2,5-dihydroxybenzylidene)-thiosemicarbazone	7qck SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×A7L; 3×GOL; 1×ZN; 3×PO4; 3×CL;
Assess
SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89	7lbr SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×ZN; 2×SO4; 1×XT7; 1×GOL;
Assess
SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83	7llf SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×ZN; 4×SO4; 2×BO3; 1×Y54;
Assess
SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-24	7lbs SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1564-1878	1×XR8; 1×ZN; 2×SO4; 3×BO3;
Assess
SARS CoV-2 PLpro in complex with inhibitor 3k	7tzj SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	1566-1875	1×S88; 4×ZN; 1×DMS;
Assess

Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
6ywk.3.A	monomer	0.84	1025-1194		100.00
Assess
6w9c.1.A	monomer	0.80	1566-1878	1×ZN;	100.00
Assess
3e9s.1.A	monomer	0.80	1564-1877	1×TTT; 1×ZN;	82.86
Assess
7cmd.4.A	monomer	0.79	1564-1878	1×TTT; 1×ZN;	100.00
Assess
2w2g.1.A	monomer	0.79	1231-1494		75.00
Assess
6wuu.2.A	monomer	0.79	1562-1879	1×ACE; 1×ZN;	99.69
Assess
2kqv.1.A	monomer	0.76	1369-1493		78.13
Assess
2kqw.1.A	monomer	0.71	1496-1550		80.22
Assess
2k87.1.A	monomer	0.69	1907-2021		81.74
Assess

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
Assess

3C-like proteinase nsp5 3264-3569; PRO_0000449639

Description	PDB ID	Oligo-state	Range	Ligands
the complex of SARS-CoV2 3CL and NB1A2	7vfa SMTL PDBe PDBe-KB PDBj PDBsum RCSB	Heteromer	3264-3563	1×SO4;
Assess
the complex of SARS-CoV2 3cl and NB2B4	7vfb SMTL PDBe PDBe-KB PDBj PDBsum RCSB	Heteromer	3275-3566
Assess
CRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE COMPLEXED WITH FRAGMENT F01	7p51 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3569	4×NA; 4×DMS; 2×5P9;
Assess
Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-04	7en8 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3569	2×J7R; 1×GOL;
Assess
Structure of the SARS-CoV-2 main protease in complex with halicin	7tuu SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3569	6×U88;
Assess
Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-02	7en9 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3569	2×J7O;
Assess
Discovery of SARS-CoV-2 3CLpro peptidomimetic inhibitors through H41-specific protein-ligand intera…	7wo1 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3569	2×3XI;
Assess
Structure of the SARS-COV-2 main protease with 337 inhibitor	7wym SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3568	2×G7L;
Assess
Structure of the SARS-COV-2 main protease with EN102 inhibitor	7wyp SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3568	2×G7O;
Assess
Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup P1211	7vlp SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3265-3567	2×4WI;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-63	7tiz SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3566	2×N63; 2×NA; 2×EDO; 2×SCN;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-14	7tia SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3566	2×XTP; 2×SCN;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB54	7tiw SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3566	2×I54; 2×PO4;
Assess
SARS-CoV-2 3CLpro	7wof SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3566	2×5IZ;
Assess
SARS-CoV-2 3CLpro	7wo3 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3566	2×59S;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-48	7tiy SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3565	2×Y48; 4×PO4; 2×EDO;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB56	7tix SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3565	2×Q56; 2×MG;
Assess
SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3w	7x6k SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3565	2×9FF;
Assess
SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3af	7x6j SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3564	2×QNC;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB46	7tiu SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3564	2×V46; 2×PO4; 2×MG;
Assess
The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1	7vth SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3564	2×7XB;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB48	7tiv SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3564	2×W48; 2×MG;
Assess
The crystal structure of SARS-CoV-2 3C-like protease in complex with a traditional Chinese Medicine…	7vic SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3564	2×ODN;
Assess
Crystal structure of SARS-CoV-2 3CL in complex with inhibitor SL-4-241	7tj0 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3564	2×S4L; 2×ACT;
Assess
Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup P212121	7vlq SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3266-3565	2×4WI;
Assess
crystal structure of SARS-CoV-2 3CL protease	7v7m SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3264-3563
Assess
The crystal structure of SARS-CoV-2 3CL protease in complex with compound 3	7vu6 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	homo-2-mer	3266-3564	2×7YY;
Assess
A dual Inhibitor Against Main Protease	7v1t SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	3264-3568	1×5IL;
Assess
SARS-COV2 Main Protease in complex with inhibitor MG-131	7z0p SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	3264-3567	1×I8H; 1×NA;
Assess
SARS-COV2 Main Protease in complex with inhibitor MG78	7ql8 SMTL PDBe PDBe-KB PDBj PDBsum RCSB	monomer	3264-3564	1×I70; 1×CL; 2×NA;
Assess

Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
5rfv.1.B	homo-2-mer	0.91	3264-3567	2×T8J;	100.00
Assess
5r7z.1.B	homo-2-mer	0.90	3264-3567	2×HWH;	100.00
Assess
6lu7.1.B	homo-2-mer	0.89	3264-3569		100.00
Assess
2z9j.1.A	homo-2-mer	0.89	3264-3567	2×DTZ;	96.08
Assess
6y2g.1.A	homo-2-mer	0.88	3264-3566	1×GLY; 2×O6K;	100.00
Assess
2a5i.1.B	homo-2-mer	0.87	3264-3569	2×AZP;	96.08
Assess

Non-structural protein 7 3860-3942; PRO_0000449641

Description	PDB ID	Oligo-state	Range	Ligands
Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mecha…	7eiz SMTL PDBe PDBe-KB PDBj PDBsum RCSB	Heteromer P0DTD1;	3861-3932	13×ZN; 1×MG;
Assess

Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
7jlt.1.A	monomer	0.80	3860-3938	100.00
Assess
6m71.1.B	monomer	0.80	3861-3930	100.00
Assess
2ahm.1.B	monomer	0.75	3860-3933	98.80
Assess

Non-structural protein 8 3943-4140; PRO_0000449642

Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
7jlt.1.D	monomer	0.76	4019-4135	100.00
Assess
2ahm.1.H	monomer	0.76	3944-4134	97.47
Assess
6nur.1.B	monomer	0.75	4019-4133	97.47
Assess
2ahm.1.E	monomer	0.69	3980-4134	97.47
Assess
6m71.1.D	monomer	0.69	4020-4133	100.00
Assess

Non-structural protein 9 4141-4253; PRO_0000449643

Template	Oligo-state	QMEANDisCo	Range	Trg-Tpl Seq id (%)
6w4b.1.A	homo-2-mer	0.80	4141-4253	100.00
Assess
1qz8.1.A	homo-2-mer	0.80	4143-4253	97.35
Assess
1uw7.1.B	homo-2-mer	0.75	4141-4253	97.35
Assess

Non-structural protein 10 4254-4392; PRO_0000449644

Template	Oligo-state	QMEANDisCo	Range	Ligands	Trg-Tpl Seq id (%)
2g9t.1.A	homo-12-mer	0.79	4261-4382	24×ZN;	97.12
Assess
6w4h.1.B	monomer	0.76	4271-4386	2×ZN;	100.00
Assess

Model ID	Oligo-state	Avg pLDDT	Range	Trg-Mdl Seq Id (%)

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

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

Replicase polyprotein 1a UniProtKBInterProInteractive Modelling

Available Structures

Host translation inhibitor nsp1 1-180; PRO_0000449635

Non-structural protein 2 181-818; PRO_0000449636

Papain-like protease nsp3 819-2763; PRO_0000449637

Non-structural protein 4 2764-3263; PRO_0000449638

3C-like proteinase nsp5 3264-3569; PRO_0000449639

Non-structural protein 7 3860-3942; PRO_0000449641

Non-structural protein 8 3943-4140; PRO_0000449642

Non-structural protein 9 4141-4253; PRO_0000449643

Non-structural protein 10 4254-4392; PRO_0000449644

Alignments

Background

Resolution

Replicase polyprotein 1a UniProtKB InterPro Interactive Modelling