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(-) Description

Title :  STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY AND PROTEASE INHIBITION IN NORWALK VIRUS
 
Authors :  B. V. V. Prasad, Z. Muhaxhiri, L. Deng, S. Shanker, B. Sankaran, M. K. Est T. Palzkill, Y. Song
Date :  03 Jan 13  (Deposition) - 20 Feb 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Muhaxhiri, L. Deng, S. Shanker, B. Sankaran, M. K. Estes, T. Palzkill, Y. Song, B. V. Prasad
Structural Basis Of Substrate Specificity And Protease Inhibition In Norwalk Virus.
J. Virol. V. 87 4281 2013
PubMed-ID: 23365454  |  Reference-DOI: 10.1128/JVI.02869-12

(-) Compounds

Molecule 1 - 3C-LIKE PROTEASE
    Chains: A
    EC Number: 3.4.22.66
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NORWALK VIRUS PROTEASE (UNP RESIDUES 1101-1281)
    Gene: ORF1
    Organism Common: HU/NV/NV/1968/US
    Organism Scientific: NOROVIRUS HU/1968/US
    Organism Taxid: 524364
    Strain: GI/HUMAN/UNITED STATES/NORWALK/1968
    Synonym: GENOME POLYPROTEIN
 
Molecule 2 - PEPTIDE INHIBITOR, SYC8
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
11HD1Mod. Amino AcidN-[(2S)-2-AMINO-3-HYDROXYPROPYL]ACETAMIDE
2NA1Ligand/IonSODIUM ION
3PHQ1Mod. Amino AcidBENZYL CHLOROCARBONATE
4SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
11HD2Mod. Amino AcidN-[(2S)-2-AMINO-3-HYDROXYPROPYL]ACETAMIDE
2NA-1Ligand/IonSODIUM ION
3PHQ2Mod. Amino AcidBENZYL CHLOROCARBONATE
4SCN4Ligand/IonTHIOCYANATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:2 , THR A:4 , LEU A:5 , ARG A:8 , HOH A:404BINDING SITE FOR RESIDUE SCN A 201
2AC2SOFTWARELEU A:121 , THR A:134 , GLY A:164 , HOH A:503BINDING SITE FOR RESIDUE NA A 202
3AC3SOFTWAREHIS A:50 , GLN A:172 , ALA A:173 , HOH A:390BINDING SITE FOR RESIDUE SCN A 203
4AC4SOFTWAREHIS A:30 , ILE A:109 , GLN A:110 , THR A:134 , ILE A:135 , PRO A:136 , CYS A:139 , HIS A:157 , ALA A:158 , ALA A:159 , ALA A:160 , GLU A:181BINDING SITE FOR CHAIN B OF PEPTIDE INHIBITOR

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IMQ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IMQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IMQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4IMQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(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:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhheeee..eeeee....eeeee.hhh.....ee..ee...eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee...hhhhh..eeeeee..eeeeeeeeeee.....eeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imq A  -1 GSAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQAGEGETALE 181
                                     8        18        28        38        48        58        68        78        88        98       108       118   ||  138       148       158       168       178   
                                                                                                                                                     122|                                                
                                                                                                                                                      133                                                


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4imq B   1 xLFx   4
                            |  |
                            1-PHQ
                               4-1HD
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4imz 4in1 4in2