2vdb

Structure of human serum albumin with S-naproxen and the GA module

Method: X-RAY DIFFRACTION Dmax: 96.9 Å Quality: REASONABLE

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

SERUM ALBUMIN

OrganismNot specified

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 30–608 Fragment:RESIDUES 30-608 PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN × 1 (Q51911) DKA DECANOIC ACID × 6 NPS (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:26-32% PEG 3350, 50 MM POTASSIUM PHOSPHATE, 0.1 M AMMONIUM PHOSPHATE/POTASSIUM PHOSPHATE Resolution 2.52 Å R-free 0.280

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 1–579; UniProt 30–608

PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN

PEPTOSTREPTOCOCCUS MAGNUS

UniProt Q51911

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 213–265 Fragment:RESIDUES 213-265 SERUM ALBUMIN × 1 (P02768) DKA DECANOIC ACID × 6 NPS (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:26-32% PEG 3350, 50 MM POTASSIUM PHOSPHATE, 0.1 M AMMONIUM PHOSPHATE/POTASSIUM PHOSPHATE Resolution 2.52 Å R-free 0.280

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.

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAB_PEPMA
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–55; UniProt 213–265

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 2vdb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2vdb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2vdb
Deposition date deposition_date2007-10-04
Structure title titleStructure of human serum albumin with S-naproxen and the GA module
Keywords keywords;LIPID-BINDING, METAL-BINDING, PROTEIN BINDING, PEPTIDOGLYCAN-ANCHOR, BACTERIAL ALBUMIN-BINDING, DISEASE MUTATION, THREE-HELIX BUNDLE, GA MODULE, DRUG BINDING, GLYCOPROTEIN, CLEAVAGE ON PAIR OF BASIC RESIDUES, HUMAN SERUM ALBUMIN, SECRETED, NAPROXEN, CELL WALL, GLYCATION ;; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.91
Radius of gyration Rg (electron density) rg_electron27.97
Forward intensity I(0) i077693400.00
Molecular weight molecular_weight69456.0 kDa
Excluded volume excluded_volume87047 ų
Envelope volume envelope_volume109470 ų
Hydration-shell volume shell_volume33118 ų
Envelope diameter envelope_diameter103.1
Shell Rg shell_rg34.80
Envelope Rg envelope_rg28.05
Shape Rg shape_rg27.98
Total Rg total_rg28.61
Total atoms total_atoms4872
Residues n_residues629
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 dmax96.9
Rg (real space) rg_real28.86
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real7.7690e+07
I(0) uncertainty (real space) i0_real_error1.1790e+06
Rg (reciprocal space) rg_reciprocal28.88
I(0) (reciprocal space) i0_reciprocal77690000.0000
Solution quality estimate total_estimate0.6943
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.378
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12550000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 0.979; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2vdba1
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.0 — automated matches
Domain ID domain_idd2vdba2
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.0 — automated matches
Domain ID domain_idd2vdba3
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.0 — automated matches
Domain ID domain_idd2vdbb_
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family familya.8.1.2 — GA module, an albumin-binding domain

CATH v4.4 (7 domains)

Domain ID domain_id2vdbA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id2vdbA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id2vdbA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id2vdbA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id2vdbA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id2vdbA06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id2vdbB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily40 — Albumin-binding domain

8. Citations (1)

9. Files and Curves (10)