3oqa

Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants

Method: X-RAY DIFFRACTION Dmax: 51.5 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 Protease

Human Immunodeficiency Virus 1

UniProt Q000H7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–99 Fragment:UNP residues 1-99 Mutation:T82S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;0.3-1.0M sodium chloride in the pH range 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.25 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q000H7_9HIV1
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–99; UniProt 1–99

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3oqa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3oqa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3oqa
Deposition date deposition_date2010-09-02
Structure title titleCrystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants
Keywords keywordsProtease, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.80
Radius of gyration Rg (electron density) rg_electron13.64
Forward intensity I(0) i02257080.00
Molecular weight molecular_weight10731.0 kDa
Excluded volume excluded_volume13721 ų
Envelope volume envelope_volume16555 ų
Hydration-shell volume shell_volume10661 ų
Envelope diameter envelope_diameter50.2
Shell Rg shell_rg18.86
Envelope Rg envelope_rg14.14
Shape Rg shape_rg13.68
Total Rg total_rg14.81
Total atoms total_atoms755
Residues n_residues99
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax51.5
Rg (real space) rg_real14.75
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real2.2570e+06
I(0) uncertainty (real space) i0_real_error2.8440e+04
Rg (reciprocal space) rg_reciprocal14.76
I(0) (reciprocal space) i0_reciprocal2257000.0000
Solution quality estimate total_estimate0.8423
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.6
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.115
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha739200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3oqaa_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.1 — Retroviral protease (retropepsin)

CATH v4.4 (1 domains)

Domain ID domain_id3oqaA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases

8. Citations (1)

9. Files and Curves (10)