2oev

Crystal structure of ALIX/AIP1

Method: X-RAY DIFFRACTION Dmax: 159.5 Å Quality: REASONABLE

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 1–698 Fragment:Bro1-V Domains, residues 1-698 Mutation:K268Y, K269Y No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;286 K;8% PEG 4000, 0.1M ammonium acetate, 0.1M magnesium acetate, 0.05M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K Resolution 3.30 Å R-free 0.317

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 8–705; UniProt 1–698

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 2oev

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2oev
Deposition date deposition_date2007-01-01
Structure title titleCrystal structure of ALIX/AIP1
Keywords keywordscoiled-coil, tetratricopeptide repeat, TPR, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.10
Radius of gyration Rg (electron density) rg_electron44.79
Forward intensity I(0) i092480800.00
Molecular weight molecular_weight77968.0 kDa
Excluded volume excluded_volume97923 ų
Envelope volume envelope_volume148550 ų
Hydration-shell volume shell_volume32351 ų
Envelope diameter envelope_diameter161.3
Shell Rg shell_rg41.03
Envelope Rg envelope_rg44.04
Shape Rg shape_rg44.79
Total Rg total_rg44.53
Total atoms total_atoms5486
Residues n_residues697
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 dmax159.5
Rg (real space) rg_real47.04
Rg uncertainty (real space) rg_real_error0.88
I(0) (real space) i0_real9.3230e+07
I(0) uncertainty (real space) i0_real_error1.5660e+06
Rg (reciprocal space) rg_reciprocal44.11
I(0) (reciprocal space) i0_reciprocal92410000.0000
Solution quality estimate total_estimate0.5390
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.0
Skewness Skewness skewness0.580
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha2.0000
Highest regularization parameter α highest_alpha4884000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.616; Stabil: 0.903; Sysdev: 0.000; Positv: 1.000; Valcen: 0.293; Smooth: 0.169

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id2oevA01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily280 — alix/aip1 like domains
Domain ID domain_id2oevA02
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_id2oevA03
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)