7qfe

Crystal structure of Human Serum albumin in complex with Gemfibrozil

Method: X-RAY DIFFRACTION Dmax: 91.1 Å Quality: EXCELLENT

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 MYR MYRISTIC ACID × 2 4TX 5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid × 2 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;285 K;30 mM Diethylene glycol, 30 mM triethylene glycol,30 mM Tetraethylene glycol, 30 mM Pentaethylene glycol, 50 mM Bicine, 50 mM Tris, pH 8.5, 12.%%MPD, 12.5 % PEG1000, 12.5% PEG3350 Resolution 2.20 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.

187 other PDB entries and 271 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

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 7qfe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7qfe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7qfe
Deposition date deposition_date2021-12-05
Structure title titleCrystal structure of Human Serum albumin in complex with Gemfibrozil
Keywords keywordshuman serum albumin, 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_guinier28.92
Radius of gyration Rg (electron density) rg_electron27.86
Forward intensity I(0) i074290400.00
Molecular weight molecular_weight68191.0 kDa
Excluded volume excluded_volume85696 ų
Envelope volume envelope_volume107950 ų
Hydration-shell volume shell_volume32781 ų
Envelope diameter envelope_diameter92.7
Shell Rg shell_rg34.72
Envelope Rg envelope_rg27.83
Shape Rg shape_rg27.86
Total Rg total_rg28.54
Total atoms total_atoms4770
Residues n_residues581
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 dmax91.1
Rg (real space) rg_real28.86
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real7.4290e+07
I(0) uncertainty (real space) i0_real_error1.0400e+06
Rg (reciprocal space) rg_reciprocal28.89
I(0) (reciprocal space) i0_reciprocal74290000.0000
Solution quality estimate total_estimate0.9065
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.1
Skewness Skewness skewness0.233
Kurtosis Kurtosis kurtosis-0.520
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11060000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.942

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id7qfeA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id7qfeA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id7qfeA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id7qfeA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id7qfeA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id7qfeA06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)