PDBsum entry 5c5o

Hydrolase/hydrolase inhibitor

PDB id

5c5o

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Contents

			Protein chains

					300 a.a.

			Ligands

					SDJ ×2

			Waters ×451

PDB id:

5c5o

Links

Name:

Hydrolase/hydrolase inhibitor

Title:

Structure of sars-3cl protease complex with a phenyl-beta-alanyl (s, r)-n-decalin type inhibitor

Structure:

3c-like proteinase. Chain: a, b. Synonym: 3cl-pro, 3clp. Engineered: yes. Mutation: yes. Other_details: beta-site amyloid precursor protein-converting enzyme

Source:

Human sars coronavirus. Sars-cov. Organism_taxid: 227859. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.50Å

R-factor:

0.248

R-free:

0.271

Authors:

K.Akaji,K.Teruya,Y.Shimamoto,A.Sanjho,E.Yamashita,A.Nakagawa

Key ref:

Y.Shimamoto et al. Fused-Ring structure of n-Decalin as a novel scaffold sars 3cl protease inhibitors. To be published, .

Date:

21-Jun-15

Release date:

22-Jun-16

PROCHECK

	Headers

	References

Protein chains

P0C6X7 (R1AB_CVHSA) - Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					7073 a.a. 300 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)



		Enzyme reactions

Enzyme class 2:

E.C.2.1.1.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 3:

E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine

5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L- methionine	=	5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L-homocysteine

Enzyme class 4:

E.C.2.1.1.57 - methyltransferase cap1.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺

5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L-methionine	=	5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA	+	S-adenosyl-L-homocysteine	+	H(+)

Enzyme class 5:

E.C.2.7.7.48 - RNA-directed Rna polymerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n)	+	ribonucleoside 5'-triphosphate	=	RNA(n+1)	+	diphosphate

Enzyme class 6:

E.C.2.7.7.50 - mRNA guanylyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a 5'-end diphospho-ribonucleoside in mRNA + GTP + H⁺ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate

5'-end diphospho-ribonucleoside in mRNA	+	GTP	+	H(+)	=	5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA	+	diphosphate

Enzyme class 7:

E.C.3.1.13.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 8:

E.C.3.4.19.12 - ubiquitinyl hydrolase 1.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Enzyme class 9:

E.C.3.4.22.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 10:

E.C.3.4.22.69 - Sars coronavirus main proteinase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 11:

E.C.3.6.4.12 - Dna helicase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

Enzyme class 12:

E.C.3.6.4.13 - Rna helicase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

Enzyme class 13:

E.C.4.6.1.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site