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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-1 BROADLY NEUTRALIZING ANTIBODY 2F5 IN COMPLEX WITH THE GP41 SCRAMBLEDFP-MPER SCRHYB3K CONSTRUCT GIGAFGLLGFLAAGSKK-AHX-K656NEQELLELDKWASLWN671
 
Authors :  J. -P. Julien, S. Bryson, B. G. De La Torre, D. Andreu, J. L. Nieva, E. F.
Date :  11 Jul 08  (Deposition) - 23 Jun 09  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hiv-1, Gp41, 2F5, Nmab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. De La Arada, J. P. Julien, B. G. De La Torre, N. Huarte, D. Andreu, E. F. Pai, J. L. Arrondo, J. L. Nieva
Structural Constraints Imposed By The Conserved Fusion Peptide On The Hiv-1 Gp41 Epitope Recognized By The Broadly Neutralizing Antibody 2F5.
J. Phys. Chem. B V. 113 13626 2009
PubMed-ID: 19754136  |  Reference-DOI: 10.1021/JP905965H

(-) Compounds

Molecule 1 - 2F5 FAB' LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System Cell Line: HYBRIDOMA CELLS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 2F5 FAB' HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System Cell Line: HYBRIDOMA CELLS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - SCRHYB3K CONSTRUCT
    Chains: C
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED BY FMOC CHEMISTRY. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN THE HUMAN IMMUNODEFICIENCY VIRUS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:160 , SER A:162 , SER A:176 , SER A:177 , THR A:178 , PHE B:166 , PRO B:167 , SER B:177 , LEU B:178 , SER B:179BINDING SITE FOR RESIDUE GOL A 215

(-) 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  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DRT)

(-) 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:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------3drtA02 A:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..........eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3drt A    1 ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRPEDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYECEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3drtB01 B:1-113 Immunoglobulins                                                                                            3drtB02 B:114-213 Immunoglobulins                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeee...........ee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhhhh..eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3drt B    1 RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQVVLVMTRVSPVDTATYFCAHRRGPTGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEP  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95    ||100N       110       120     ||137       147       157       167       177       187       197       207      
                                                             35A|                                             82A||              100I|||||                       126|                                                                               
                                                              35B                                              82B|               100J||||                        134                                                                               
                                                                                                                82C                100K|||                                                                                                          
                                                                                                                                    100L||                                                                                                          
                                                                                                                                     100M|                                                                                                          
                                                                                                                                      100N                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                3drt C    3 ELDKWA    8
   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 3DRT)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

2p8m 3d0l 3dro 3drq 3drv