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(-) Description

Title :  1.85A RESOLUTION STRUCTURE OF NOROVIRUS 3CL PROTEASE COMPLEX WITH A COVALENTLY BOUND DIPEPTIDYL INHIBITOR DIETHYL [(1R,2S)-2-[(N-{[(3-CHLOROBENZYL)OXY]CARBONYL}-3-CYCLOHEXYL-L-ALANYL)AMINO]-1-HYDROXY-3-(2-OXO-2H-PYRROL-3-YL)PROPYL]PHOSPHONATE
 
Authors :  S. Lovell, K. P. Battaile, N. Mehzabeen, A. C. G. Kankanamalage, Y. Kim, P. M. Weerawarna, R. A. Z. Uy, V. C. Damalanka, S. R. Mandadapu, K. R. All W. C. Groutas, K. -O. Chang
Date :  16 Dec 14  (Deposition) - 25 Mar 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Protease, Norovirus, Norwalk Virus, Antiviral Inhibitors, Dipeptidyl Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Galasiti Kankanamalage, Y. Kim, P. M. Weerawarna, R. A. Uy, V. C. Damalanka, S. R. Mandadapu, K. R. Alliston, N. Mehzabeen, K. P. Battaile, S. Lovell, K. O. Chang, W. C. Groutas
Structure-Guided Design And Optimization Of Dipeptidyl Inhibitors Of Norovirus 3Cl Protease. Structure-Activity Relationships And Biochemical, X-Ray Crystallographic, Cell-Based, And In Vivo Studies.
J. Med. Chem. V. 58 3144 2015
PubMed-ID: 25761614  |  Reference-DOI: 10.1021/JM5019934

(-) Compounds

Molecule 1 - 3C-LIKE PROTEASE
    Chains: A
    EC Number: 3.4.22.66
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: ORF1
    Organism Common: HU/NV/NV/1968/US
    Organism Scientific: NORWALK VIRUS (STRAIN GI/HUMAN/UNITED STATES/NORWALK/1968)
    Organism Taxid: 524364
    Strain: GI/HUMAN/UNITED STATES/NORWALK/1968

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
13ZR1Ligand/IonDIETHYL [(1R,2S)-2-[(N-{[(3-CHLOROBENZYL)OXY]CARBONYL}-3-CYCLOHEXYL-L-ALANYL)AMINO]-1-HYDROXY-3-(2-OXO-2H-PYRROL-3-YL)PROPYL]PHOSPHONATE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
13ZR1Ligand/IonDIETHYL [(1R,2S)-2-[(N-{[(3-CHLOROBENZYL)OXY]CARBONYL}-3-CYCLOHEXYL-L-ALANYL)AMINO]-1-HYDROXY-3-(2-OXO-2H-PYRROL-3-YL)PROPYL]PHOSPHONATE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
13ZR2Ligand/IonDIETHYL [(1R,2S)-2-[(N-{[(3-CHLOROBENZYL)OXY]CARBONYL}-3-CYCLOHEXYL-L-ALANYL)AMINO]-1-HYDROXY-3-(2-OXO-2H-PYRROL-3-YL)PROPYL]PHOSPHONATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:30 , GLU A:54 , GLN A:110 , THR A:134 , CYS A:139 , HIS A:157 , ALA A:158 , ALA A:159 , ALA A:160 , VAL A:168 , HOH A:369 , HOH A:377 , HOH A:379 , HOH A:388binding site for residue 3ZR A 201
2AC2SOFTWARETHR A:161 , SER A:163 , ASN A:165 , THR A:166 , HOH A:424binding site for residue SO4 A 202

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:77 -A:154

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XBB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4XBB)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeee..eeeee....eeeee.hhh.....ee..ee...eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee..........eeeeee..eeeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xbb A  -1 HMAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQA 173
                                     8        18        28        38        48        58        68        78        88        98       108       118   ||  138       148       158       168     
                                                                                                                                                     122|                                        
                                                                                                                                                      133
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4XBB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XBB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XBB)

(-) Gene Ontology  (22, 22)

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  4xbb
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  POLG_NVN68 | Q83883
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        POLG_NVN68 | Q83883: 2fyq 2fyr 2lnc 3ur6 3ur9 4imq 4imz 4in1 4in2 4inh 4xbc 4xbd 5dg6 5dgj 5e0g 5e0h 5e0j 5t6d 5t6f 5t6g 5tg1 5tg2

(-) Related Entries Specified in the PDB File

4xbc 4xbd