6l4k

Human serum albumin-Palmitic acid-Cu compound

Method: X-RAY DIFFRACTION Dmax: 152.0 Å Quality: REASONABLE

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 27–607 Not recorded PLM PALMITIC ACID × 6 E5O 2-bromanyl-9-ethyl-~{N},~{N},7-trimethyl-3-thia-1$l^{4},5,6$l^{4},10-tetraza-2$l^{4}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),4,6,9,11-pentaen-4-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;293 K;PEG3350, 50 mM potassium phosphate (pH 7.5), 5% glycerol, and 4% DMSO. Resolution 2.09 Å R-free 0.290
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain I; UniProt 27–607 Not recorded PLM PALMITIC ACID × 6 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;293 K;PEG3350, 50 mM potassium phosphate (pH 7.5), 5% glycerol, and 4% DMSO. Resolution 2.09 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.

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 1–581; UniProt 27–607 Author chain I; PDBConstruct 1–581; UniProt 27–607

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 6l4k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6l4k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6l4k
Deposition date deposition_date2019-10-17
Structure title titleHuman serum albumin-Palmitic acid-Cu compound
Keywords keywordsComplex, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.32
Radius of gyration Rg (electron density) rg_electron41.43
Forward intensity I(0) i0248116000.00
Molecular weight molecular_weight129960.0 kDa
Excluded volume excluded_volume163310 ų
Envelope volume envelope_volume225070 ų
Hydration-shell volume shell_volume47242 ų
Envelope diameter envelope_diameter160.4
Shell Rg shell_rg44.24
Envelope Rg envelope_rg41.08
Shape Rg shape_rg41.45
Total Rg total_rg41.55
Total atoms total_atoms9106
Residues n_residues1162
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 dmax152.0
Rg (real space) rg_real41.61
Rg uncertainty (real space) rg_real_error1.95
I(0) (real space) i0_real2.4810e+08
I(0) uncertainty (real space) i0_real_error4.9610e+06
Rg (reciprocal space) rg_reciprocal41.32
I(0) (reciprocal space) i0_reciprocal248000000.0000
Solution quality estimate total_estimate0.6078
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.0
Skewness Skewness skewness0.598
Kurtosis Kurtosis kurtosis0.111
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27080000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.684; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.919; Smooth: 0.903

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6l4ka1
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6l4ka2
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6l4ka3
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6l4ki1
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6l4ki2
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6l4ki3
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like

CATH v4.4 (9 domains)

Domain ID domain_id6l4kA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kI01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kI03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6l4kI04
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)