9yz5

human FicD bound with farnesyl pyrophosphate

Method: X-RAY DIFFRACTION Dmax: 96.4 Å Quality: EXCELLENT

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

Protein adenylyltransferase FICD

Homo sapiens

UniProt Q9BVA6

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 105–433 Chain B; UniProt 105–433 Not recorded FPP FARNESYL DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;100 mM Bis-Tris propane (pH 7.5), 200 mM potassium sodium tartrate, and 21% PEG 3350 Resolution 2.58 Å R-free 0.290

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.

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

View Construct and Data Evidence
UniProt name FICD_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–330; UniProt 105–433 Author chain B; PDBConstruct 2–330; UniProt 105–433

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 9yz5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yz5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yz5
Deposition date deposition_date2025-10-30
Structure title titlehuman FicD bound with farnesyl pyrophosphate
Keywords keywordsAMPylation, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.61
Radius of gyration Rg (electron density) rg_electron29.76
Forward intensity I(0) i092114300.00
Molecular weight molecular_weight76444.0 kDa
Excluded volume excluded_volume96090 ų
Envelope volume envelope_volume125290 ų
Hydration-shell volume shell_volume35164 ų
Envelope diameter envelope_diameter96.8
Shell Rg shell_rg37.10
Envelope Rg envelope_rg29.02
Shape Rg shape_rg29.77
Total Rg total_rg30.44
Total atoms total_atoms5378
Residues n_residues658
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 dmax96.4
Rg (real space) rg_real30.52
Rg uncertainty (real space) rg_real_error0.65
I(0) (real space) i0_real9.2110e+07
I(0) uncertainty (real space) i0_real_error1.3470e+06
Rg (reciprocal space) rg_reciprocal30.56
I(0) (reciprocal space) i0_reciprocal92120000.0000
Solution quality estimate total_estimate0.9086
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary94.5
Skewness Skewness skewness0.176
Kurtosis Kurtosis kurtosis-0.563
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12500000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.947

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)