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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV EPITOPE-SCAFFOLD 4E10_1XIZA_S0_001_N
 
Authors :  M. A. Holmes
Date :  15 Jan 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Epitope-Scaffold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. E. Correia, Y. E. Ban, M. A. Holmes, H. Xu, K. Ellingson, Z. Kraft, C. Carrico, E. Boni, D. N. Sather, C. Zenobia, K. Y. Burke, T. Bradley-Hewitt, J. F. Bruhn-Johannsen, O. Kalyuzhniy, D. Baker, R. K. Strong, L. Stamatatos, W. R. Schief
Computational Design Of Epitope-Scaffolds Allows Induction Of Antibodies Specific For A Poorly Immunogenic Hiv Vaccine Epitope.
Structure V. 18 1116 2010
PubMed-ID: 20826338  |  Reference-DOI: 10.1016/J.STR.2010.06.010

(-) Compounds

Molecule 1 - PUTATIVE PHOSPHOTRANSFERASE SYSTEM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630
    Synonym: 4E10_1XIZA_S0_001_N (T117), MANNITOL/FRUCTOSE-SPECIFIC IIA DOMAIN CONTAINING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:13 , ARG A:15 , HOH A:234BINDING SITE FOR RESIDUE PO4 A 162
2AC2SOFTWARESER A:27 , ASN A:29 , ASP A:30BINDING SITE FOR RESIDUE PO4 A 163
3AC3SOFTWARESER B:27 , ASN B:29 , ASP B:30 , HOH B:206BINDING SITE FOR RESIDUE PO4 B 162

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LF6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:67 -Pro A:68
2Glu B:67 -Pro B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LF6)

(-) Exons   (0, 0)

(no "Exon" information available for 3LF6)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains d3lf6a_ A: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..hhh.eeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..ee.....eee....hhhhh...eeeeeeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lf6 A   7 NAMQGIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDSKYVRQNAISVGILAEPVNFEDAGGEPDPVPVRVVFMLALGNWFDITNVLWWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRIS 160
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156    


Chain B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains d3lf6b_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhh.eeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..ee.....eee....hhhhh...eeeeeeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lf6 B   4 HHHNAMQGIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDSKYVRQNAISVGILAEPVNFEDAGGEPDPVPVRVVFMLALGNWFDITNVLWWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRIS 160
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LF6)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LF6)

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3lef 3lf9 3lg7 3lh2 3lhp