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

(-) Description

Title :  ANTI-HUMAN CYTOMEGALOVIRUS (HCMV) FAB KE5 WITH EPITOPE PEPTIDE AD-2S1
 
Authors :  S. Bryson, L. Risnes, S. Damgupta, C. A. Thomson, R. Pfoh, J. W. Schrader
Date :  09 Oct 12  (Deposition) - 23 Oct 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Fab Fragment, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bryson, L. Risnes, S. Damgupta, C. A. Thomson, J. W. Schrader, E. F. Pai
Multitasking Immunoglobulin V-Genes And Somatic Diversity I Cdr3 Loops Generate Binding Sites For Chemically Distinct Antigens From Bacterial And Viral Pathogens.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FAB KE5
    Chains: A
    Fragment: FAB FRAGMENT KE5
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTIBODY KE5
    Chains: B
    Fragment: AD-2S1 EPTIOPE
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GLYCOPROTEIN B
    Chains: P
    Engineered: YES
    Organism Common: HHV-5
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10359
    Other Details: SYNTHESIZED PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:59 , ARG A:61BINDING SITE FOR RESIDUE CL A 301
2AC2SOFTWAREASP A:50 , ARG A:91 , ASN P:5BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWARETRP A:35 , ALA A:51 , SER A:65 , PHE A:71 , THR A:72BINDING SITE FOR RESIDUE CL A 303
4AC4SOFTWAREGLU A:1 , VAL A:2 , GLN A:90 , ASN A:93 , PRO A:95A , HOH A:417BINDING SITE FOR RESIDUE CL A 304
5AC5SOFTWAREVAL B:12 , GLN B:13BINDING SITE FOR RESIDUE CL B 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:196

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Trp A:94 -Pro A:95
3Pro A:95 -Pro A:95A
4Tyr A:140 -Pro A:141
5Phe B:146 -Pro B:147
6Glu B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HHA)

(-) Sequences/Alignments

Asymmetric/Biological 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:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee..eeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hha A    1 EVVLTQSPATLSLSPGERATISCRASQSVGGYLTWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISGLEPEDFAIYYCQQRGNWPPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149     ||162       172       182       192       202       212  
                                                                                                                         95A                                                         155|                                                       
                                                                                                                                                                                      159                                                       


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.ee....ee...eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh...eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hha B    1 QVQLVESGGGVVQPGRSLRLSCAASGFTFSNHGMHWVRQAPGKRLEWVAVISYDGRHEHYADLVKGRFTISRDNSKNTLYLQMNSLRAEDRALYFCAREGLSRDNSGFTGLIDYWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158||     169       179       189       199       209      
                                                                              52A                            82A||               100A|||||||                                                        159|                                                      
                                                                                                              82B|                100B||||||                                                         161                                                      
                                                                                                               82C                 100C|||||                                                                                                                  
                                                                                                                                    100D||||                                                                                                                  
                                                                                                                                     100E|||                                                                                                                  
                                                                                                                                      100F||                                                                                                                  
                                                                                                                                       100G|                                                                                                                  
                                                                                                                                        100H                                                                                                                  


Chain P from PDB  Type:PROTEIN  Length:10
                                           
               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
                4hha P    1 ETIYNTTLKY   10
                                    10
   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 4HHA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ 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 ]
 
  Cis Peptide Bonds
    Glu B:148 - Pro B:149   [ RasMol ]  
    Phe B:146 - Pro B:147   [ RasMol ]  
    Pro A:95 - Pro A:95A  [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Trp A:94 - Pro A:95   [ RasMol ]  
    Tyr A:140 - Pro A:141   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4hha
    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
  Q9YKI2_HCMV | Q9YKI2
    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
  Q9YKI2_HCMV | Q9YKI2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4HHA)

(-) Related Entries Specified in the PDB File

4hh9 ANTI-HUMAN CYTOMEGALOVIRUS (HCMV) FAB KE5
4hie ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102
4hih ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102 WITH BOUND RHAMNOSE
4hii ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102 WITH BOUND RHAMNOSE-GALACTOSE
4hij ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102 WITH BOUND L- RHAMNOSE-(1-2)-ALPHA-D-GALACTOSE-(3-O)-PHOSPHATE-2-GLYCEROL