2F58

IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120) (MN ISOLATE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.

Stanfield, R.Cabezas, E.Satterthwait, A.Stura, E.Profy, A.Wilson, I.

(1999) Structure Fold.Des. 7: 131-142

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The third hypervariable (V3) loop of HIV-1 gp120 has been termed the principal neutralizing determinant (PND) of the virus and is involved in many aspects of virus infectivity. The V3 loop is required for viral entry into the cell via membrane fusion ...

    The third hypervariable (V3) loop of HIV-1 gp120 has been termed the principal neutralizing determinant (PND) of the virus and is involved in many aspects of virus infectivity. The V3 loop is required for viral entry into the cell via membrane fusion and is believed to interact with cell surface chemokine receptors on T cells and macrophages. Sequence changes in V3 can affect chemokine receptor usage, and can, therefore, modulate which types of cells are infected. Antibodies raised against peptides with V3 sequences can neutralize laboratory-adapted strains of the virus and inhibit syncytia formation. Fab fragments of these neutralizing antibodies in complex with V3 loop peptides have been studied by X-ray crystallography to determine the conformation of the V3 loop.


    Organizational Affiliation

    The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN))
L
216Mus musculusMutation(s): 0 
Find proteins for P01666 (Mus musculus)
Go to UniProtKB:  P01666
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN))
H
228N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HIV-1 GP120)
P
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARN
Query on ARN

Download SDF File 
Download CCD File 
P
1-IMINO-5-PENTANONE
C5 H9 N O
UWHJGSVKWBLVLI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.080α = 90.00
b = 114.720β = 90.00
c = 49.530γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
MERLOTphasing
UCSD-systemdata reduction
X-PLORrefinement
X-PLORmodel building
UCSD-systemdata scaling
UCSD-systemdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description