2AMD: SARS_CoV Mpro

Crystal Structure Of SARS_CoV Mpro in Complex with an Inhibitor N9. Determined by X-ray diffraction at 1.85 Å resolution. Released 13 Sept 2005.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: SARS coronavirus
Chains: 2
Atoms: 5,223
Mol. weight: 69.84 kDa
Ligands: 9IN
Released: 13 Sept 2005

Explore 2AMD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2AMD contains 34 α-helices and 40 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7	1	1
α-helix	8-9	2
α-helix	11-14	4
β-strand	17-22	6	2
β-strand	25-32	8	2
β-strand	35-39	5	2
α-helix	40-43	4
α-helix	54-59	6
α-helix	63-65	3
β-strand	66-70	5	2
β-strand	73-75	3	2
β-strand	77-83	7	2
β-strand	86-91	6	2
α-helix	98-99	2
β-strand	101-103	3	3
β-strand	111-118	8	3
β-strand	121-129	9	3
β-strand	136	1	3
β-strand	148-153	6	3
β-strand	156-166	11	3
β-strand	172-175	4	3
α-helix	180	1
β-strand	181	1	3
α-helix	194-197	4
β-strand	199	1	4
α-helix	201-213	13
α-helix	227-234	8
α-helix	235-237	3
β-strand	239	1	4
α-helix	240-242	3
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	5
β-strand	284	1	5
α-helix	293-301	9

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	3
α-helix	11-14	4
β-strand	17-22	6	6
β-strand	25-32	8	6
β-strand	35-39	5	6
α-helix	40-43	4
α-helix	46-48	3
α-helix	54-59	6
α-helix	63-65	3
β-strand	66-70	5	6
β-strand	73-75	3	6
α-helix	76	1
β-strand	77-83	7	6
β-strand	86-91	6	6
α-helix	98-99	2
β-strand	100-103	4	1
α-helix	106-107	2
β-strand	111-118	8	1
β-strand	121-129	9	1
β-strand	136	1	1
β-strand	148-153	6	1
β-strand	156-166	11	1
β-strand	172-175	4	1
α-helix	180	1
β-strand	181	1	1
β-strand	199	1	7
α-helix	201-213	13
α-helix	227-234	8
α-helix	235-237	3
β-strand	239	1	7
α-helix	240-242	3
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	8
β-strand	284	1	8
α-helix	293-301	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3C-like proteinase	A, B	protein	311	SARS coronavirus	P0C6U8

Sequence of entity 1 (A, B), FASTA

>2AMD_1 3C-like proteinase (chains A, B)
GPLGSSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYE
DLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVL
ACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGT
DLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAM
KYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFD
VVRQCSGVTFQ

Ligands and cofactors

ID	Name	Formula	Copies
9IN	N-(3-furoyl)-D-valyl-L-valyl-N~1~-((1R,2Z)-4-ethoxy-4-oxo-1-{[(3S)-2-oxopyrroli…	C32 H49 N5 O8	2

Primary citation

Design of Wide-Spectrum Inhibitors Targeting Coronavirus Main Proteases. Yang, H., Xie, W., Xue, X. et al. PLoS Biol (2005) 3:324-334. DOI 10.1371/journal.pbio.0030324 · PubMed

Other PDB entries of the same protein (UniProt P0C6U8), best resolution first:

6XHN 1.38 Å, Covalent complex of SARS-CoV main protease with 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)…
4M0W 1.4 Å, Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
6XHO 1.45 Å, Covalent complex of SARS-CoV main protease with ethyl (4R)-4-({N-[(4-methoxy-1H-indol-2-y…
6XHL 1.47 Å, Covalent complex of SARS-CoV main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)…
4MDS 1.6 Å, Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as…
2H2Z 1.6 Å, Crystal structure of SARS-CoV main protease with authentic N and C-termini
7LMG 1.6 Å, SARS-CoV-1 3CLPro in complex with N-(4-(1H-imidazol-4-yl)phenyl)-2-(1H-benzo[d][1,2,3]tri…
7RC1 1.63 Å, X-ray Structure of SARS-CoV main protease covalently modified by compound GRL-0686
5Y3E 1.65 Å, Crystal structure of SARS coronavirus papain-like protease in complex with glycerol
5Y3Q 1.65 Å, Crystal structure of SARS coronavirus papain-like protease conjugated with…
6W2A 1.65 Å, 1.65 A resolution structure of SARS-CoV 3CL protease in complex with inhibitor 7j
7LMJ 1.69 Å, SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(3-chlorobenzyl)-N…

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