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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 8 PROTEASE WITH AN IRREVERSIBLE VINYL SULFONE INHIBITOR
 
Authors :  P. Grosche, F. Sirockin, A. Mac Sweeney, P. Ramage, P. Erbel, S. Melkko A. Bernardi, N. Hughes, D. Ellis, K. Combrink, N. Jarousse, E. Altmann
Date :  13 Nov 14  (Deposition) - 14 Jan 15  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cysteine Protease, Deubiquitinase, Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Grosche, F. Sirockin, A. Mac Sweeney, P. Ramage, P. Erbel, S. Melkko, A. Bernardi, N. Hughes, D. Ellis, K. D. Combrink, N. Jarousse, E. Altmann
Structure-Based Design And Optimization Of Potent Inhibitor Of The Adenoviral Protease.
Bioorg. Med. Chem. Lett. V. 25 438 2015
PubMed-ID: 25571794  |  Reference-DOI: 10.1016/J.BMCL.2014.12.057

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, C
    EC Number: 3.4.22.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: L3
    Organism Common: HADV-8
    Organism Scientific: HUMAN ADENOVIRUS D SEROTYPE 8
    Organism Taxid: 31545
 
Molecule 2 - PVI
    Chains: B, D
    Engineered: YES
    Fragment: UNP RESIDUES 223-233
    Organism Common: HADV-8
    Organism Scientific: HUMAN ADENOVIRUS D SEROTYPE 8
    Organism Taxid: 31545
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13VK2Ligand/IonN-[(2S)-2-(3,5-DICHLOROPHENYL)-2-(ETHYLAMINO)ACETYL]-3-METHYL-L-VALYL-N-[3-(METHYLSULFONYL)PROPYL]GLYCINAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13VK1Ligand/IonN-[(2S)-2-(3,5-DICHLOROPHENYL)-2-(ETHYLAMINO)ACETYL]-3-METHYL-L-VALYL-N-[3-(METHYLSULFONYL)PROPYL]GLYCINAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13VK1Ligand/IonN-[(2S)-2-(3,5-DICHLOROPHENYL)-2-(ETHYLAMINO)ACETYL]-3-METHYL-L-VALYL-N-[3-(METHYLSULFONYL)PROPYL]GLYCINAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:1 , GLY A:2 , SER A:3 , SER A:4 , GLU A:5 , THR A:24 , ASN A:44 , ALA A:46 , ARG A:48 , GLY A:51 , GLY A:52 , VAL A:53 , HIS A:54 , TRP A:55 , PHE A:73 , TYR A:84 , GLN A:115 , SER A:119 , CYS A:122 , MET A:201binding site for residue 3VK A 301
2AC2SOFTWAREGLN A:162 , GLY C:2 , SER C:3 , SER C:4 , GLU C:5 , GLN C:6 , THR C:24 , HIS C:25 , ASP C:26 , ASN C:44 , ALA C:46 , ARG C:48 , GLY C:51 , GLY C:52 , VAL C:53 , HIS C:54 , TRP C:55 , PHE C:73 , TYR C:84 , GLN C:115 , SER C:119 , ALA C:120 , ALA C:121 , GLY C:123 , LEU C:124 , PHE C:125 , CYS C:126 , MET C:201 , HOH C:405binding site for Di-peptide 3VK C 301 and CYS C 122

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:104 -B:309
2C:104 -D:309

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WX6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WX6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WX6)

(-) Exons   (0, 0)

(no "Exon" information available for 4WX6)

(-) 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 ...hhhhhhhhhhhh.hhh.eeeee.............eeeeee..hhhhh...eeeeeee....eeeee.....hhhhhhhhhh..hhhhhhhhhhhhh...eeeeeee.ee.......hhhhhhhhhhhhhh..................ee.hhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wx6 A   1 SGSSEQELAAIVRDLGCGPYFLGTHDKRFPGFLAGNKLACAIVNTAGRETGGVHWLAFGWNPRSRTCYMFDPFGFSDRRLKQIYSFEYEAMLRRSALALSPDRCLSLEQSTQTVQGPDSAACGLFCCMFLHAFVHWPDRPMDGNPTMNLLTGVPNGMLQSPQVLPTLRRNQEKLYRFLAHHSPYFRSHRAAIEHATAFDKMKQL 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4wx6 B 300 GVKSLKRRRCY 310
                                   309 


Chain C from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....eeeee.............eeeeee..hhhhh...eeeeeee....eeeee.....hhhhhhhhhh..hhhhhhhhhhhhh...eeeeeee.ee.......hhhhhhhhhhhhhhhh.........hhhhh..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wx6 C   1 SGSSEQELAAIVRDLGCGPYFLGTHDKRFPGFLAGNKLACAIVNTAGRETGGVHWLAFGWNPRSRTCYMFDPFGFSDRRLKQIYSFEYEAMLRRSALALSPDRCLSLEQSTQTVQGPDSAACGLFCCMFLHAFVHWPDRPMDGNPTMNLLTGVPNGMLQSPQVLPTLRRNQEKLYRFLAHHSPYFRSHRAAIEHATAFDKMKQL 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4wx6 D 300 GVKSLKRRRCY 310
                                   309
   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 4WX6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WX6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WX6)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  4wx6
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 Related Entries

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

UniProtKB/TrEMBL
        B9A5C1_ADE08 | B9A5C1: 4piq 4pis 4wx4 4wx7
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(-) Related Entries Specified in the PDB File

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