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(-) Description

Title :  CRYSTAL STRUCTURE OF WEST NILE VIRUS NS2B-NS3 PROTEASE IN COMPLEX WITH A CAPPED DIPEPTIDE BORONATE INHIBITOR
 
Authors :  R. Hilgenfeld, L. Zhang
Date :  24 Feb 16  (Deposition) - 14 Dec 16  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Antivirus Agents, Peptides, West Nile Virus, Boronic Acid, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Nitsche, L. Zhang, L. F. Weigel, J. Schilz, D. Graf, R. Bartenschlager, R. Hilgenfeld, C. D. Klein
Peptide-Boronic Acid Inhibitors Of Flaviviral Proteases: Medicinal Chemistry And Structural Biology.
J. Med. Chem. V. 60 511 2017
PubMed-ID: 27966962  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01021

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN,SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3
    Chains: A, B, C
    EC Number: 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: WNV
    Organism Scientific: WEST NILE VIRUS
    Organism Taxid: 11082

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
16A83Ligand/Ion((R)-1-((S)-3-(4-(AMINOMETHYL)PHENYL)-2-BENZAMIDOPROPANEAMIDO)-4-GUANIDINOBUTYL)BORONIC ACID,CYCLIC DOUBLE ESTER WITH GLYCEROL
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16A81Ligand/Ion((R)-1-((S)-3-(4-(AMINOMETHYL)PHENYL)-2-BENZAMIDOPROPANEAMIDO)-4-GUANIDINOBUTYL)BORONIC ACID,CYCLIC DOUBLE ESTER WITH GLYCEROL
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
16A81Ligand/Ion((R)-1-((S)-3-(4-(AMINOMETHYL)PHENYL)-2-BENZAMIDOPROPANEAMIDO)-4-GUANIDINOBUTYL)BORONIC ACID,CYCLIC DOUBLE ESTER WITH GLYCEROL
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
16A81Ligand/Ion((R)-1-((S)-3-(4-(AMINOMETHYL)PHENYL)-2-BENZAMIDOPROPANEAMIDO)-4-GUANIDINOBUTYL)BORONIC ACID,CYCLIC DOUBLE ESTER WITH GLYCEROL
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3GOL1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:82 , GLY A:83 , ASN A:84 , ALA A:1036 , HIS A:1051 , ASP A:1129 , TYR A:1130 , THR A:1132 , GLY A:1133 , THR A:1134 , SER A:1135 , GLY A:1151 , ASN A:1152 , GLY A:1153 , ILE A:1155 , TYR A:1161 , HOH A:1381 , HOH A:1450 , ARG C:74 , LYS C:1117 , GLU C:1122 , HOH C:1348binding site for residue 6A8 A 1201
2AC2SOFTWAREASP B:82 , GLY B:83 , ASN B:84 , ALA B:1036 , HIS B:1051 , TYR B:1068 , ASP B:1129 , TYR B:1130 , THR B:1132 , GLY B:1133 , THR B:1134 , SER B:1135 , GLY B:1151 , ASN B:1152 , GLY B:1153 , ILE B:1155 , TYR B:1161 , HOH B:1313 , HOH B:1326 , HOH B:1411 , HOH B:1427binding site for residue 6A8 B 1201
3AC3SOFTWAREGLY B:70 , SER B:71 , ASN B:1090 , ASP B:1093 , ASN B:1143 , HOH B:1359binding site for residue DMS B 1202
4AC4SOFTWARELYS A:1015 , ARG C:56 , ASP C:1017 , THR C:1019 , TYR C:1023 , HOH C:1303binding site for residue GOL C 1202
5AC5SOFTWAREASP C:82 , GLY C:83 , ASN C:84 , ALA C:1036 , GLY C:1037 , ALA C:1038 , HIS C:1051 , THR C:1052 , ASP C:1129 , TYR C:1130 , GLY C:1133 , THR C:1134 , GLY C:1136 , SER C:1137 , TYR C:1150 , GLY C:1151 , ASN C:1152 , GLY C:1153 , ILE C:1155 , TYR C:1161 , HOH C:1337 , HOH C:1345 , HOH C:1405 , HOH C:1441binding site for Di-peptide 6A8 C 1201 and SER C 1135

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IDK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:1014 -Lys A:1015
2Gly B:1001 -Gly B:1002

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IDK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IDK)

(-) Exons   (0, 0)

(no "Exon" information available for 5IDK)

(-) 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:204
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee........ee.....eeeeee.....eee..eee.............eeeeeeee....eeeeeeeeee..eeeehhhhhh...eee..eee.eeeee....eeee...............eeeee.......eeeee..eeee....eeeee...........eee.....eeee...eee.....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5idk A   51 DMWIERTADITWESDAEITGSSERVDVRLDDDGNFQLMGGVLWDTPSPKKGDTTTGVYRIMTRGLLGSYQAGAGVMVEGVFHTLWHTTKGAALMSGEGRLDPYWGSVKEDRLCYGGPWKLQHKWNGHDEVQMIVVEPGKNVKNVQTKPGVFKTPEGEIGAVTLDYPTGTSGSPIVDKNGDVIGLYGNGVIMPNGSYISAIVQGE 1169
                                    60        70        80      1002      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165    
                                                                88|     1010|                                                                                                                                                           
                                                               1001      1014                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee........ee.....eeeeee.....eee...ee............eeeeeeeee..eeeeeeeeeee..eeeeehhhhh...eee..eee.eeeee....eeee...............eeeee.......eeeee..eeeee..eeeeee...........eee.....eeee...eee.....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5idk B   50 TDMWIERTADITWESDAEITGSSERVDVRLDDDGNFQLMGGVLWDTEYKKGDTTTGVYRIMTRGLLGSYQAGAGVMVEGVFHTLWHTTKGAALMSGEGRLDPYWGSVKEDRLCYGGPWKLQHKWNGHDEVQMIVVEPGKNVKNVQTKPGVFKTPEGEIGAVTLDYPTGTSGSPIVDKNGDVIGLYGNGVIMPNGSYISAIVQGE 1169
                                    59        69        79      1001     |1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165    
                                                                 88|  1007|                                                                                                                                                             
                                                                1001   1012                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........ee.....eeeeee.....eee..eee..............eeeeeeeee..eeeeeeeeeee..eeeehhhhhh...eee..eee.eeeee....eeee...............eeeee.......eeeee..eeeee..eeeeee...........eee.....eeee...eee.....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5idk C   51 DMWIERTADITWESDAEITGSSERVDVRLDDDGNFQLMGGVLWDTPKEYKKGDTTTGVYRIMTRGLLGSYQAGAGVMVEGVFHTLWHTTKGAALMSGEGRLDPYWGSVKEDRLCYGGPWKLQHKWNGHDEVQMIVVEPGKNVKNVQTKPGVFKTPEGEIGAVTLDYPTGTSGSPIVDKNGDVIGLYGNGVIMPNGSYISAIVQGE 1169
                                    60        70        80      1002     |1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164     
                                                                88|   1008|                                                                                                                                                              
                                                               1001    1011
   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 5IDK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IDK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IDK)

(-) Gene Ontology  (66, 66)

Asymmetric Unit(hide GO term definitions)

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