Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CYPOVIRUS POLYHEDRA MUTANT WITH DELETION OF SER193 AND ALA194
 
Authors :  S. Abe, H. Tabe, H. Ijiri, K. Yamashita, K. Hirata, H. Mori, T. Ueno
Date :  07 Aug 16  (Deposition) - 15 Feb 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  In Vivo Protein Crystal, Polyhedra, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Abe, H. Tabe, H. Ijiri, K. Yamashita, K. Hirata, K. Atsumi, T. Shimoi M. Akai, H. Mori, S. Kitagawa, T. Ueno
Crystal Engineering Of Self-Assembled Porous Protein Materials In Living Cells
Acs Nano V. 11 2410 2017
PubMed-ID: 28094987  |  Reference-DOI: 10.1021/ACSNANO.6B06099

(-) Compounds

Molecule 1 - POLYHEDRIN
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Mutation: YES
    Organism Common: BMCPV
    Organism Scientific: BOMBYX MORI CYPOVIRUS 1
    Organism Taxid: 110829
    Synonym: C-POLYHEDRIN,CYPOVIRUS POLYHEDRIN PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric Unit (6, 9)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL1Ligand/IonCHLORIDE ION
4CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
5EDO3Ligand/Ion1,2-ETHANEDIOL
6MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (4, 72)
No.NameCountTypeFull Name
1ACE12Mod. Amino AcidACETYL GROUP
2ATP12Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4CTP12Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
5EDO36Ligand/Ion1,2-ETHANEDIOL
6MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:2 , LEU A:31 , HOH A:493binding site for residue CL A 301
2AC2SOFTWARECTP A:305 , HOH A:464binding site for residue MG A 302
3AC3SOFTWAREATP A:304 , HOH A:401 , HOH A:417binding site for residue MG A 303
4AC4SOFTWARETYR A:25 , LYS A:152 , LYS A:154 , ARG A:155 , ASP A:156 , GLY A:157 , LYS A:184 , MG A:303 , HOH A:401 , HOH A:412 , HOH A:417 , HOH A:421 , HOH A:497binding site for residue ATP A 304
5AC5SOFTWAREHIS A:76 , ASN A:77 , ASP A:78 , SER A:79 , TYR A:80 , ASP A:81 , ASP A:96 , ARG A:98 , MG A:302 , HOH A:464 , HOH A:477binding site for residue CTP A 305
6AC6SOFTWAREASN A:28 , SER A:114 , PRO A:115 , GLN A:138 , PRO A:231 , HOH A:461 , HOH A:462binding site for residue EDO A 306
7AC7SOFTWAREARG A:151 , LYS A:152 , LYS A:154 , LEU A:233 , ASN A:237 , SER A:239 , HOH A:497binding site for residue EDO A 307
8AC8SOFTWAREASP A:3 , GLY A:46 , PHE A:100 , ALA A:216 , GLU A:217 , HOH A:488binding site for residue EDO A 308

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GQJ)

(-) 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:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeee.eeeeeehhhhhh........hhhhhhhhhhhhhh................eeeeee...eeeeeeeeeee........hhhhh.....hhhhheeeee..eeeeeeeeee........eeeeeeee.........hhhhhhhhhhhheeeeeee.hhhhhhhhhhhhhh..ee.....ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gqj A   1 xADVAGTSNRDFRGREQRLFNSEQYNYNNSLNGEVSVWVYAYYSDGSVLVINKNSQYKVGISETFKALKEYREGQHNDSYDEYEVNQSIYYPNGGDARKFHSNAKPRAIQIIFSPSVNVRTIKMAKGNAVSVPDEYLQRSHPWEATGIKYRKIKRDGEIVGYSHYFELPHEYNSISLAVSGVHKNPSSYNGHNVMDVFQSCDLALRFCNRYWAELELVNHYISPNAYPYLDINNHSYGVALSNRQ 248
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190||     203       213       223       233       243     
                            |                                                                                                                                                                                          190||                                                     
                            1-ACE                                                                                                                                                                                       192|                                                     
                                                                                                                                                                                                                         195
   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 5GQJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gqj)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5gqj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYHD_CPVBM | P11041
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PYHD_CPVBM | P11041
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PYHD_CPVBM | P11041: 5a9b 5axu 5axv 5exy 5exz 5gqi 5gqk 5gql 5gqm 5gqn

(-) Related Entries Specified in the PDB File

5gqi 5gqk 5gql 5gqm 5gqn