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(-) Description

Title :  CRYSTAL STRUCTURE OF BACULOVIRUS P35
 
Authors :  A. J. Fisher, W. P. Delacruz, S. J. Zoog, C. L. Schneider, P. D. Friesen
Date :  18 Sep 98  (Deposition) - 01 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Apoptosis, P35, Cell Death, Baculovirus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Fisher, W. Cruz, S. J. Zoog, C. L. Schneider, P. D. Friesen
Crystal Structure Of Baculovirus P35: Role Of A Novel Reactive Site Loop In Apoptotic Caspase Inhibition.
Embo J. V. 18 2031 1999
PubMed-ID: 10205157  |  Reference-DOI: 10.1093/EMBOJ/18.8.2031
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P35
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BACULOVIRUS
    Expression System Taxid: 562
    Expression System Vector Type: BACULOVIRUS
    Organism Scientific: AUTOGRAPHA CALIFORNICA NUCLEOPOLYHEDROVIRUS
    Organism Taxid: 46015

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:17 , LYS A:59 , PO4 A:301 , HOH A:317 , ARG C:80BINDING SITE FOR RESIDUE PO4 A 1
2AC2SOFTWAREPO4 A:1 , ARG A:66 , LYS A:70 , EDO A:303 , HOH A:354 , ARG C:80BINDING SITE FOR RESIDUE PO4 A 301
3AC3SOFTWAREHIS B:283 , SER C:257BINDING SITE FOR RESIDUE PO4 B 301
4AC4SOFTWARESER A:216 , SER A:287 , ALA A:288 , SER B:216 , ALA B:288BINDING SITE FOR RESIDUE EDO A 302
5AC5SOFTWAREARG A:17 , LYS A:70 , PO4 A:301BINDING SITE FOR RESIDUE EDO A 303
6AC6SOFTWAREARG B:17 , LEU B:63 , ARG B:66 , ILE B:67 , LYS B:70BINDING SITE FOR RESIDUE EDO B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P35)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:5 -Pro A:6
2Phe B:5 -Pro B:6
3Phe C:5 -Pro C:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P35)

(-) Exons   (0, 0)

(no "Exon" information available for 1P35)

(-) 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:299
 aligned with P35_NPVAC | P08160 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:299
                                                                                                                                                                                                                                                                                                                                   299 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       | 
            P35_NPVAC     2 CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKVDEQFDQLERDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIK-   -
               SCOP domains d1p35a_ A: Baculovirus p35 protein                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1p35A00 A:2-300 Baculovirus P35                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeeeeeeee..eeeeeeee..........eeeeeee.eeeeee......hhhhhhhhhhhhhhhh.......................eeeeeehhhhhhhhhhhhhhh....hhhhhhhhhh.hhhh.......eeeeeee.........eeeeeeeee...eeee...........eeeeeeeee......hhhhhhhhh............eeeeeeee...eeeeeeeeeeee.........eeeee..eeeeee....eeeeeeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p35 A   2 CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKVDEQFDQLERDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIKA 300
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291         


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with P35_NPVAC | P08160 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
            P35_NPVAC     2 CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKVDEQFDQLERDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIK 299
               SCOP domains d1p35b_ B: Baculovirus p35 protein                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1p35B00 B:2-299 Baculovirus P35                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeeeeeeee..eeeeeeee..........eeeeeee.eeeeee......hhhhhhhhhhhhhhhh.......................eeeeeehhhhhh.hhhhhhhh....hhhhhhhhhh.hhh........eeeeeee.........eeeeeeeee...eeee...........eeeeeeeeee.....hhhhhhhhh............eeeeeeee...eeeeeeeeeeeee.......eeeeee..eeeeee....eeeeeeeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p35 B   2 CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKVDEQFDQLERDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIK 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        


Chain C from PDB  Type:PROTEIN  Length:295
 aligned with P35_NPVAC | P08160 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:299
                                                                                                                                                                                                                                                                                                                                   299 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       | 
            P35_NPVAC     2 CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKVDEQFDQLERDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIK-   -
               SCOP domains d1p35c_ C: Baculovirus p35 protein                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1p35C00 C:2-300 Baculovirus P35                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeeeeeeee..eeeeeeee..........eeeeeee...eeee......hhhhhhhhhhhhhhhh............----.......eeeeeehhhhhhhhhhhhhhh....hhhhhhhhhh.hhh........eeeeeee.........eeeeeee.....eeee...........eeeeeeeee......hhhhhhhhh............eeeeeeee....eeeeeeeeeeee.......eeeeee..eeeeee....eeeeeeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p35 C   2 CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKVDEQFDQLERDYSDQMDGFH----YFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIKA 300
                                    11        21        31        41        51        61        71        81        |-   |   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291         
                                                                                                                   90   95
   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  (1, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P35)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (P35_NPVAC | P08160)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0039526    modulation by virus of host apoptotic process    Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P35_NPVAC | P08160: 1i3p 1i3s 1i4e 2fun

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1P35)