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1B3A | pdb_00001b3a
TOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE POTENT ANTI-HIV PROTEIN AOP-RANTES
- PDB DOI: https://doi.org/10.2210/pdb1B3A/pdb
- Classification: ANTI-HIV PROTEIN
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 1998-12-07 Released: 1999-04-23
- Deposition Author(s): Wilken, J., Hoover, D., Thompson, D.A., Barlow, P.N., Mcsparron, H., Picard, L., Wlodawer, A., Lubkowski, J., Kent, S.B.H.
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)
wwPDB Validation3D Report Full Report
Literature
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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
- PubMed: 9889151 Search on PubMed
- 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.
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Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (AOP)
Biological Assembly 1
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (AOP)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Biological Assembly 2
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (AOP)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 2 assigned by authors.
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
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PROTEIN (RANTES) | 67 | Homo sapiens | Mutation(s): 0 Gene Names: CCL5 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P13501 GTEx: ENSG00000271503 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13501 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AOP Download:Ideal Coordinates CCD File | F [auth A], H [auth B] | PENTYLOXYAMINO-ACETALDEHYDE C7 H15 N O2 PKNNPRVGISCRDL-UHFFFAOYSA-N | 👁 Image | ||
| SO4 Download:Ideal Coordinates CCD File
| C [auth A], D [auth A], E [auth A], G [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | 👁 Image | ||
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)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 23.635 | α = 90 |
| b = 56.307 | β = 90 |
| c = 94.03 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| AMoRE | phasing |
| SHELXL-97 | refinement |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 1999-04-23 Deposition Author(s): Wilken, J., Hoover, D., Thompson, D.A., Barlow, P.N., Mcsparron, H., Picard, L., Wlodawer, A., Lubkowski, J., Kent, S.B.H.
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
