2oex

Structure of ALIX/AIP1 V Domain

Method: X-RAY DIFFRACTION Dmax: 109.4 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 360–702 Chain B; UniProt 360–702 Fragment:V Domain, residues 359-702 Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;277 K;14% PEG 3350, 0.16M magnesium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.58 Å R-free 0.302

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 9–351; UniProt 360–702 Author chain B; PDBConstruct 9–351; 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 2oex

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2oex
Deposition date deposition_date2007-01-01
Structure title titleStructure of ALIX/AIP1 V Domain
Keywords keywordsCoiled-coil, 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_guinier33.42
Radius of gyration Rg (electron density) rg_electron32.79
Forward intensity I(0) i0100942000.00
Molecular weight molecular_weight77145.0 kDa
Excluded volume excluded_volume95821 ų
Envelope volume envelope_volume140270 ų
Hydration-shell volume shell_volume37341 ų
Envelope diameter envelope_diameter113.0
Shell Rg shell_rg37.89
Envelope Rg envelope_rg31.88
Shape Rg shape_rg32.80
Total Rg total_rg33.23
Total atoms total_atoms5391
Residues n_residues675
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 dmax109.4
Rg (real space) rg_real33.40
Rg uncertainty (real space) rg_real_error1.18
I(0) (real space) i0_real1.0090e+08
I(0) uncertainty (real space) i0_real_error1.7500e+06
Rg (reciprocal space) rg_reciprocal33.41
I(0) (reciprocal space) i0_reciprocal100900000.0000
Solution quality estimate total_estimate0.8736
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.6
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.253
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5036000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.847

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id2oexA01
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_id2oexA02
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
Domain ID domain_id2oexB01
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_id2oexB02
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)