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⇱ RCSB PDB - 1B3A: TOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE POTENT ANTI-HIV PROTEIN AOP-RANTES


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Computed Structure Models (CSM)

 1B3A | pdb_00001b3a

TOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE POTENT ANTI-HIV PROTEIN AOP-RANTES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.241 (Depositor) 
  • R-Value Work: 
    0.173 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

This is version 1.5 of the entry. See complete history

Literature

Total chemical synthesis and high-resolution crystal structure of the potent anti-HIV protein AOP-RANTES.

Wilken, J.Hoover, D.Thompson, D.A.Barlow, P.N.McSparron, H.Picard, L.Wlodawer, A.Lubkowski, J.Kent, S.B.

(1999) Chem Biol 6: 43-51

  • DOI: https://doi.org/10.1016/S1074-5521(99)80019-2
  • Primary Citation Related Structures: 
    1B3A

  • PubMed Abstract: 

    RANTES is a CC-type chemokine protein that acts as a chemoattractant for several kinds of leukocytes, playing an important pro-inflammatory role. Entry of human immunodeficiency virus-1 (HIV-1) into cells depends on the chemokine receptor CCR5. RANTES binds CCR5 and inhibits HIV-1 entry into peripheral blood cells. Interaction with chemokine receptors involves a distinct set of residues at the amino terminus of RANTES. This finding was utilized in the development of a chemically modified aminooxypentane derivative of RANTES, AOP-RANTES, that was originally produced from the recombinant protein using semisynthetic methods. AOP-RANTES has been produced by a novel total chemical synthesis that provides efficient, direct access to large amounts of this anti-HIV protein analog. The crystal structure of chemically synthesized AOP-RANTES has been solved and refined at 1.6 A resolution. The protein is a dimer, with the amino-terminal pentane oxime moiety clearly defined. Total chemical synthesis of AOP-RANTES provides a convenient method of producing the multi-milligram quantities of this protein needed to investigate the molecular basis of receptor binding and antiviral activity. This work provides the first truly high-resolution structure of a RANTES protein, although the structure of RANTES was known from previous nuclear magnetic resonance (NMR) determinations.


  • Organizational Affiliation
    • Gryphon Sciences, 250 East Grand Avenue, Suite 90, South San Francisco,CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 16.22 kDa 
  • Atom Count: 1,357 
  • Modeled Residue Count: 134 
  • Deposited Residue Count: 134 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (RANTES)
A, B
67Homo sapiensMutation(s): 0 
Gene Names: CCL5
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UniProt & NIH Common Fund Data Resources
Find proteins for P13501 (Homo sapiens)
Explore P13501 
Go to UniProtKB:  P13501
PHAROS:  P13501
GTEx:  ENSG00000271503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13501
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.241 (Depositor) 
  • R-Value Work:  0.173 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.635α = 90
b = 56.307β = 90
c = 94.03γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-23
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.