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(-) Description

Title :  THE CRYSTAL STRUCTURE OF XMRV PROTEASE COMPLEXED WITH ACETYL-PEPSTATIN
 
Authors :  M. Li, A. Wlodawer
Date :  30 Apr 12  (Deposition) - 01 Aug 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,J,M,P
Biol. Unit 1:  A,B,J,M  (1x)
Biol. Unit 2:  A,B,P  (1x)
Keywords :  Beta Sheet, Dimer, Protease, Acetyl-Pepstain, Virus, Hydrolase-Hydrol Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Matuz, J. Motyan, M. Li, A. Wlodawer
Inhibition Of Xmrv And Hiv-1 Proteases By Pepstatin A And Acetyl-Pepstatin.
Febs J. V. 279 3276 2012
PubMed-ID: 22804908  |  Reference-DOI: 10.1111/J.1742-4658.2012.08714.X

(-) Compounds

Molecule 1 - PUTATIVE GAG-PRO-POL POLYPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST-521
    Expression System Strain: BL21(DE3)TONA PRARE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 533-657
    Gene: GAG-POL
    Organism Scientific: DG-75 MURINE LEUKEMIA VIRUS
    Organism Taxid: 114654
    Strain: PCDNA3.1-XMRV-VP63
 
Molecule 2 - ACETYL-PEPSTATIN
    Chains: J, M, P
    Engineered: YES
    Organism Common: CHAINIA
    Organism Scientific: STREPTOMYCES
    Organism Taxid: 1883
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABJMP
Biological Unit 1 (1x): ABJM 
Biological Unit 2 (1x): AB  P

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2FMT1Ligand/IonFORMIC ACID
3STA4Mod. Amino AcidSTATINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2FMT1Ligand/IonFORMIC ACID
3STA2Mod. Amino AcidSTATINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2FMT-1Ligand/IonFORMIC ACID
3STA2Mod. Amino AcidSTATINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:53 , STA M:4 , ALA M:5BINDING SITE FOR RESIDUE FMT M 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16
2Glu B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EXH)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..eeeeeee.......ee......eeeeeeeee....eeeeeee..eeeee..eeeee..ee.......eehhhhhhhhh.eee......eee.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4exh A  11 EPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQV 124
                                    20        30        40        50        60        70        80        90       100       110       120    


Chain B from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeee.......ee......eeeeeeeee....eeeeeee..eeee....eeee..ee.......eehhhhhhhhh.eeeee..eeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4exh B  11 EPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPL 122
                                    20        30        40        50        60        70        80        90       100       110       120  


Chain J from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .ee.. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4exh J   1 xVVxA   5
                            |  | 
                            1-ACE
                               4-STA


Chain M from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .ee.. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4exh M   1 xVVxA   5
                            |  | 
                            |  | 
                            1-ACE
                               4-STA


Chain P from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .ee.ee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4exh P   1 xVVxAx   6
                            |  | |
                            |  | |
                            1-ACE|
                               4-STA
                                 6-STA
   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 4EXH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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        Q9E7M1_9GAMR | Q9E7M1: 3slz 3sm1 3sm2

(-) Related Entries Specified in the PDB File

3sm1