Biological Assembly 1

Protein Symmetry: Cyclic - C2 (View in 3D)

Protein Stoichiometry: Homo 2-mer - A2

Macromolecule Content

• Unique protein chains: 1

3AO2

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

• DOI: 10.2210/pdb3ao2/pdb

• Classification: VIRAL PROTEIN / TRANSFERASE INHIBITOR
• Deposited: 2010-09-20 Released: 2011-03-16
• Deposition author(s): Wielens, J., Chalmers, D.K., Headey, S.J., Parker, M.W., Scanlon, M.J.
• Organism: Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): 7

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.217
• R-Value Work: 0.187

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: VIRAL PROTEIN / TRANSFERASE INHIBITOR

Total Structure Weight: 37370.12

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
AVX	A, B	3-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl- 1H-pyrazol-5-amine C11 H10 Br N3 O2 CYGCZVZRSOGLAB-UHFFFAOYSA-N	Poseview Image of AVX in 3AO2 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
DTT	B	2,3-DIHYDROXY-1,4-DITHIOBUTANE 1,4-DITHIOTHREITOL (Synonym) C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N	Poseview Image of DTT in 3AO2 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
DTV	A	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C4 H10 O2 S2 VHJLVAABSRFDPM-QWWZWVQMSA-N	Poseview Image of DTV in 3AO2 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
CD	A, B	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N	Poseview Image of CD in 3AO2 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L	Poseview Image of SO4 in 3AO2 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 3AO2 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N	Poseview Image of MG in 3AO2 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AVX	N/A in BindingDB Kd: 170000 nM  BindingMOAD Kd: 170000 nM  PDBbind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.217
• R-Value Work: 0.187
• Space Group: P 3₂

Unit Cell:

Length (Å)	Angle (°)
a = 49.16	α = 90.00
b = 49.16	β = 90.00
c = 103.12	γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2010-09-20
• Released Date: 2011-03-16
• Deposition author(s): Wielens, J., Chalmers, D.K., Headey, S.J., Parker, M.W., Scanlon, M.J.

Revision History

• Version 1_0: 2011-03-16
  

  Type: Initial release

• Version 1_1: 2011-07-13
  

  Type: Version format compliance