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(-) Description

Title :  CRYSTAL STRUCTURE OF EV71 3C PROTEINASE IN COMPLEX WITH COMPOUND 3
 
Authors :  C. Wu, L. Zhang, P. Li, Q. Cai, X. Peng, N. Li, Y. Cai, J. Li, T. Lin
Date :  12 Sep 15  (Deposition) - 30 Mar 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hand, Foot And Mouth Disease, 3C Proteinase, Peptidomimetics, Drug Design, Rupintrivir, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wu, L. Zhang, P. Li, Q. Cai, X. Peng, K. Yin, X. Chen, H. Ren, S. Zhong, Y. Weng, Y. Guan, S. Chen, J. Wu, J. Li, T. Lin
Fragment-Wise Design Of Inhibitors To 3C Proteinase From Enterovirus 71
Biochim. Biophys. Acta V. 1860 1299 2016
PubMed-ID: 26987809  |  Reference-DOI: 10.1016/J.BBAGEN.2016.03.017

(-) Compounds

Molecule 1 - 3C PROTEINASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROVIRUS A71
    Organism Taxid: 39054

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
15E84Ligand/IonETHYL (2Z,4S)-4-{[(2S)-2-METHYL-3-PHENYLPROPANOYL]AMINO}-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15E81Ligand/IonETHYL (2Z,4S)-4-{[(2S)-2-METHYL-3-PHENYLPROPANOYL]AMINO}-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15E81Ligand/IonETHYL (2Z,4S)-4-{[(2S)-2-METHYL-3-PHENYLPROPANOYL]AMINO}-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
15E81Ligand/IonETHYL (2Z,4S)-4-{[(2S)-2-METHYL-3-PHENYLPROPANOYL]AMINO}-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
15E81Ligand/IonETHYL (2Z,4S)-4-{[(2S)-2-METHYL-3-PHENYLPROPANOYL]AMINO}-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:39 , HIS A:40 , LEU A:127 , SER A:128 , THR A:142 , LYS A:143 , ALA A:144 , GLY A:145 , CYS A:147 , HIS A:161 , ILE A:162 , GLY A:163 , GLY A:164binding site for residue 5E8 A 201
2AC2SOFTWAREPHE B:25 , THR B:26 , ARG B:39 , HIS B:40 , GLU B:71 , LEU B:127 , SER B:128 , THR B:142 , LYS B:143 , ALA B:144 , GLY B:145 , GLN B:146 , GLY B:148 , GLY B:149 , HIS B:161 , ILE B:162 , GLY B:163 , GLY B:164 , HOH B:349 , HOH B:387binding site for Di-peptide 5E8 B 201 and CYS B 147
3AC3SOFTWAREPHE C:25 , THR C:26 , ARG C:39 , HIS C:40 , GLU C:71 , LEU C:127 , SER C:128 , THR C:142 , LYS C:143 , ALA C:144 , GLY C:145 , GLN C:146 , GLY C:148 , GLY C:149 , HIS C:161 , ILE C:162 , GLY C:163 , GLY C:164 , HOH C:335 , HOH C:354binding site for Di-peptide 5E8 C 201 and CYS C 147
4AC4SOFTWAREPHE D:25 , THR D:26 , ARG D:39 , HIS D:40 , LEU D:127 , SER D:128 , THR D:142 , LYS D:143 , ALA D:144 , GLY D:145 , GLN D:146 , GLY D:148 , GLY D:149 , HIS D:161 , ILE D:162 , GLY D:163 , GLY D:164 , HOH D:334 , HOH D:355binding site for Di-peptide 5E8 D 201 and CYS D 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DP4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DP4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DP4)

(-) Exons   (0, 0)

(no "Exon" information available for 5DP4)

(-) 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:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeee..eeeeeeeee..eeeee.hhh...eeee..eeeeeeeeeeee.....eeeeeeeee........hhhhh......eeeeeeee.......eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeee....eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dp4 A   0 MGPSLDFALSLLRRNVRQVQTDQGHFTMLGVRDRLAVLPRHSQPGKTIWIEHKLVNILDAVELVDEQGVNLELTLITLDTNEKFRDITKFIPENISTASDATLVINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVTSVGKVIGIHIGGNGRQGFCAGLKRSYFA 180
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 


Chain B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeee..eeeeeeeee..eeeee.hhh...eeee..eeeeeeeeeeee.....eeeeeeeee........hhhhh......eeeeeeee.......eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeee....eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dp4 B   0 MGPSLDFALSLLRRNVRQVQTDQGHFTMLGVRDRLAVLPRHSQPGKTIWIEHKLVNILDAVELVDEQGVNLELTLITLDTNEKFRDITKFIPENISTASDATLVINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVTSVGKVIGIHIGGNGRQGFCAGLKRSYFA 180
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 


Chain C from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeee..eeeeeeeee..eeeee.hhh...eeee..eeeeeeeeeeee.....eeeeeeeee........hhhhh......eeeeeeee.......eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeee....eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dp4 C   0 MGPSLDFALSLLRRNVRQVQTDQGHFTMLGVRDRLAVLPRHSQPGKTIWIEHKLVNILDAVELVDEQGVNLELTLITLDTNEKFRDITKFIPENISTASDATLVINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVTSVGKVIGIHIGGNGRQGFCAGLKRSYFA 180
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 


Chain D from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeee..eeeeeeeee..eeeee.hhh...eeee..eeeeeeeeeeee.....eeeeeeeee........hhhhh......eeeeeeee.......eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeee....eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dp4 D   0 MGPSLDFALSLLRRNVRQVQTDQGHFTMLGVRDRLAVLPRHSQPGKTIWIEHKLVNILDAVELVDEQGVNLELTLITLDTNEKFRDITKFIPENISTASDATLVINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVTSVGKVIGIHIGGNGRQGFCAGLKRSYFA 180
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   Legend:   → Mismatch (orange background)
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  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 5DP4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DP4)

(-) Gene Ontology  (37, 37)

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 Related Entries

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

UniProtKB/TrEMBL
        A9XG43_9ENTO | A9XG43: 4fvb 4fvd 4ghq 4ght 5c1u 5c1x 5c1y 5c20 5dp3 5dp5 5dp6 5dp7 5dp8 5dp9 5dpa

(-) Related Entries Specified in the PDB File

5dp3 5dp5 5dp6 5dp7 5dp8 5dp9 5dpa