3OVN
Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase
- PDB DOI: https://doi.org/10.2210/pdb3OVN/pdb
- Classification: VIRAL PROTEIN/TRANSFERASE INHIBITOR
- Organism(s): Human immunodeficiency virus 1
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2010-09-16 Released: 2011-03-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.249 
- R-Value Work: 0.211 
- R-Value Observed: 0.213 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
POL polyprotein | 163 | Human immunodeficiency virus 1 | Mutation(s): 4  Gene Names: pol | ||
UniProt | |||||
Find proteins for Q72498 (Human immunodeficiency virus 1) Explore Q72498  Go to UniProtKB:  Q72498 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q72498 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MPV Query on MPV | E [auth A], I [auth B] | 1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine C8 H9 N3 S NFTITKUYTQZKIZ-UHFFFAOYSA-N | |||
CD Query on CD | F [auth A], G [auth A], J [auth B], K [auth B] | CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N | |||
SO4 Query on SO4 | D [auth A], H [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900003 Query on PRD_900003 | C | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.249 
- R-Value Work: 0.211 
- R-Value Observed: 0.213 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.75 | α = 90 |
b = 59.704 | β = 90 |
c = 81.818 | γ = 90 |
Software Name | Purpose |
---|---|
Blu-Ice | data collection |
AMoRE | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2011-03-09  Deposition Author(s): Wielens, J., Chalmers, D.K., Headey, S.J., Deadman, J.J., Rhodes, D.K., Parker, M.W., Scanlon, M.J.
Revision History (Full details and data files)
- Version 1.0: 2011-03-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary