3guc

Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP

Method: X-RAY DIFFRACTION Dmax: 80.5 Å Quality: GOOD

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

Ubiquitin-like modifier-activating enzyme 5

Homo sapiens

UniProt Q9GZZ9

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 57–329 Chain B; UniProt 57–329 Not recorded ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.2;287 K;1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE,0.1 M SODIUM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K Resolution 2.25 Å R-free 0.255

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.

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

View Construct and Data Evidence
UniProt name UBA5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 20–292; UniProt 57–329 Author chain B; PDBConstruct 20–292; UniProt 57–329

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 3guc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3guc
Deposition date deposition_date2009-03-29
Structure title titleHuman Ubiquitin-activating Enzyme 5 in Complex with AMPPNP
Keywords keywordsROSSMANN FOLD, ATP-BINDING, UBL CONJUGATION PATHWAY, TRANSFERASE, Structural Genomics, Structural Genomics Consortium, SGC; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.20
Radius of gyration Rg (electron density) rg_electron24.13
Forward intensity I(0) i044445000.00
Molecular weight molecular_weight50710.0 kDa
Excluded volume excluded_volume63122 ų
Envelope volume envelope_volume77260 ų
Hydration-shell volume shell_volume27041 ų
Envelope diameter envelope_diameter81.8
Shell Rg shell_rg31.13
Envelope Rg envelope_rg24.36
Shape Rg shape_rg24.14
Total Rg total_rg24.91
Total atoms total_atoms3542
Residues n_residues463
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 dmax80.5
Rg (real space) rg_real25.23
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real4.4440e+07
I(0) uncertainty (real space) i0_real_error6.5460e+05
Rg (reciprocal space) rg_reciprocal25.22
I(0) (reciprocal space) i0_reciprocal44440000.0000
Solution quality estimate total_estimate0.8903
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1
Skewness Skewness skewness0.402
Kurtosis Kurtosis kurtosis-0.359
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5198000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.940

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3gucA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3gucB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain

8. Citations (1)

9. Files and Curves (10)