2ojq

Crystal structure of Alix V domain

Method: X-RAY DIFFRACTION Dmax: 102.8 Å Quality: GOOD

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

Programmed cell death 6-interacting protein

Homo sapiens

UniProt Q8WUM4

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 360–702 Fragment:V domain, residues 360-702 Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;13-15% PEG 6000, 6-10% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K Resolution 2.87 Å R-free 0.318

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.

18 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDC6I_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–348; UniProt 360–702

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 2ojq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ojq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ojq
Deposition date deposition_date2007-01-13
Structure title titleCrystal structure of Alix V domain
Keywords keywordshelical, APOPTOSIS; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.58
Radius of gyration Rg (electron density) rg_electron29.16
Forward intensity I(0) i026289500.00
Molecular weight molecular_weight38692.0 kDa
Excluded volume excluded_volume48086 ų
Envelope volume envelope_volume67515 ų
Hydration-shell volume shell_volume21096 ų
Envelope diameter envelope_diameter108.9
Shell Rg shell_rg33.37
Envelope Rg envelope_rg29.18
Shape Rg shape_rg29.15
Total Rg total_rg29.65
Total atoms total_atoms2704
Residues n_residues339
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 dmax102.8
Rg (real space) rg_real29.81
Rg uncertainty (real space) rg_real_error1.15
I(0) (real space) i0_real2.6290e+07
I(0) uncertainty (real space) i0_real_error4.6400e+05
Rg (reciprocal space) rg_reciprocal29.71
I(0) (reciprocal space) i0_reciprocal26290000.0000
Solution quality estimate total_estimate0.8513
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3
Skewness Skewness skewness0.467
Kurtosis Kurtosis kurtosis-0.291
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1946000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.760; Smooth: 0.849

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2ojqA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily560 — alix/aip1 in complex with the ypdl late domain
Domain ID domain_id2ojqA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily50 — alix/aip1 like domains

8. Citations (1)

9. Files and Curves (10)