9upd

Crystal structure of human serum albumin complex with nateglinide

Method: X-RAY DIFFRACTION Dmax: 114.5 Å Quality: GOOD

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

Serum albumin

Homo sapiens

UniProt P02768

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 25–609 Not recorded A1L9H (2R)-3-phenyl-2-[(4-propan-2-ylcyclohexyl)carbonylamino]propanoic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;32% PEG 3350, 50mM potassium phosphate pH 7.0 Resolution 2.80 Å R-free 0.287
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 25–609 Not recorded A1L9H (2R)-3-phenyl-2-[(4-propan-2-ylcyclohexyl)carbonylamino]propanoic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;32% PEG 3350, 50mM potassium phosphate pH 7.0 Resolution 2.80 Å R-free 0.287

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.

187 other PDB entries and 270 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ALBU_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–585; UniProt 25–609 Author chain B; PDBConstruct 1–585; UniProt 25–609

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 9upd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9upd
Deposition date deposition_date2025-04-28
Structure title titleCrystal structure of human serum albumin complex with nateglinide
Keywords keywordsHuman serum albumin, nateglinide, complex, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.82
Radius of gyration Rg (electron density) rg_electron35.39
Forward intensity I(0) i0446387000.00
Molecular weight molecular_weight112490.0 kDa
Excluded volume excluded_volume108060 ų
Envelope volume envelope_volume205240 ų
Hydration-shell volume shell_volume48962 ų
Envelope diameter envelope_diameter124.0
Shell Rg shell_rg41.63
Envelope Rg envelope_rg34.27
Shape Rg shape_rg35.36
Total Rg total_rg35.78
Total atoms total_atoms8457
Residues n_residues1118
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 dmax114.5
Rg (real space) rg_real35.75
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real4.4640e+08
I(0) uncertainty (real space) i0_real_error6.2550e+06
Rg (reciprocal space) rg_reciprocal35.80
I(0) (reciprocal space) i0_reciprocal446400000.0000
Solution quality estimate total_estimate0.8954
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.2
Skewness Skewness skewness0.262
Kurtosis Kurtosis kurtosis-0.393
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25470000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.848

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)