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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL FRAGMENT OF THE BACTERIOPHAGE PHI92 MEMBRANE-PIERCING PROTEIN GP138
 
Authors :  C. Browning, M. Shneider, P. G. Leiman
Date :  26 Nov 10  (Deposition) - 22 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Biol. Unit 3:  A,B  (3x)
Keywords :  Beta-Helix, Ob-Fold, Phage Baseplate, Iron-Binding, Cell Membrane Piercing, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Browning, M. M. Shneider, V. D. Bowman, D. Schwarzer, P. G. Leiman
Phage Pierces The Host Cell Membrane With The Iron-Loaded Spike.
Structure V. 20 326 2012
PubMed-ID: 22325780  |  Reference-DOI: 10.1016/J.STR.2011.12.009

(-) Compounds

Molecule 1 - GENE PRODUCT 138
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: 834 (DE3)
    Expression System Taxid: 562
    Fragment: C-TERMINAL FRAGMENT
    Organism Scientific: BACTERIOPHAGE PHI92
    Organism Taxid: 38018

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B
Biological Unit 3 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2NA7Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:223 , HIS B:225BINDING SITE FOR RESIDUE FE B 1
2AC2SOFTWAREHIS A:223 , HIS A:225BINDING SITE FOR RESIDUE FE A 2
3AC3SOFTWAREARG B:211 , MET B:212 , ASP B:214 , LEU B:220 , HIS B:221BINDING SITE FOR RESIDUE NA B 2
4AC4SOFTWAREASP A:209 , ARG A:211 , LYS A:241 , HOH A:267BINDING SITE FOR RESIDUE NA A 3
5AC5SOFTWARETHR A:205 , HOH A:265 , HOH A:279 , HOH A:282BINDING SITE FOR RESIDUE NA A 4
6AC6SOFTWAREGLY A:217 , GLY A:219 , THR A:222 , HIS A:223 , HOH A:294BINDING SITE FOR RESIDUE NA A 5
7AC7SOFTWARETHR A:207 , ASP A:209 , ARG A:211 , LYS A:241BINDING SITE FOR RESIDUE NA A 6
8AC8SOFTWAREGLY B:217 , GLY B:219 , THR B:222 , HIS B:223BINDING SITE FOR RESIDUE NA B 10
9AC9SOFTWAREGLY A:216 , GLY A:217 , GLY A:244 , HOH A:294 , HOH A:647BINDING SITE FOR RESIDUE NA A 11

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PQH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PQH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PQH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PQH)

(-) Exons   (0, 0)

(no "Exon" information available for 3PQH)

(-) 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:107
 aligned with H3JQU8_9VIRU | H3JQU8 from UniProtKB/TrEMBL  Length:127

    Alignment length:107
                                    29        39        49        59        69        79        89        99       109       119       
         H3JQU8_9VIRU    20 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 126
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee.....eeeee....eeeee..eeeeee...eeeeee..eeeee...eee..eee.....ee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3pqh A 138 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 244
                                   147       157       167       177       187       197       207       217       227       237       


Chain A from PDB  Type:PROTEIN  Length:107
 aligned with I7HXF9_9CAUD | I7HXF9 from UniProtKB/TrEMBL  Length:245

    Alignment length:107
                                   147       157       167       177       187       197       207       217       227       237       
         I7HXF9_9CAUD   138 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 244
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee.....eeeee....eeeee..eeeeee...eeeeee..eeeee...eee..eee.....ee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3pqh A 138 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 244
                                   147       157       167       177       187       197       207       217       227       237       


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with H3JQU8_9VIRU | H3JQU8 from UniProtKB/TrEMBL  Length:127

    Alignment length:107
                                    29        39        49        59        69        79        89        99       109       119       
         H3JQU8_9VIRU    20 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 126
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee.....eeeee....eeeee..eeeeee...eeeeee..eeeee...eee..eee.....ee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3pqh B 138 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 244
                                   147       157       167       177       187       197       207       217       227       237       


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with I7HXF9_9CAUD | I7HXF9 from UniProtKB/TrEMBL  Length:245

    Alignment length:107
                                   147       157       167       177       187       197       207       217       227       237       
         I7HXF9_9CAUD   138 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 244
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee.....eeeee....eeeee..eeeeee...eeeeee..eeeee...eee..eee.....ee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3pqh B 138 EKVIISNNKQTYASFDPNGNISVYNTQGMKIDMTPNSIVLTDAGGGKLTLQGGTMTYKGGTVNLNGLTITPDGRMTDSGGIGLHTHTHPVRGVETGGSTVTSDKPNG 244
                                   147       157       167       177       187       197       207       217       227       237
   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 3PQH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PQH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PQH)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3PQH)

 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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pqh)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3pqh
    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
  H3JQU8_9VIRU | H3JQU8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  I7HXF9_9CAUD | I7HXF9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  H3JQU8_9VIRU | H3JQU8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  I7HXF9_9CAUD | I7HXF9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        I7HXF9_9CAUD | I7HXF9: 3pqi

(-) Related Entries Specified in the PDB File

3pqi CRYSTAL STRUCTURE OF BACTERIOPHAGE GP138 MEMBRANE-PIERCING PROTEIN