6m58

Crystal structure of a complex between human serum albumin and the antibody Fab SL335

Method: X-RAY DIFFRACTION Dmax: 148.5 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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–609 Not recorded Heavy chain of the SL335 antibody fab × 1 Light chain of the SL335 antibody Fab × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;PEG 4000, Tris, pH 8.5, glycerol, sodium acetate Resolution 2.95 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 25–609 Not recorded Heavy chain of the SL335 antibody fab × 1 Light chain of the SL335 antibody Fab × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;PEG 4000, Tris, pH 8.5, glycerol, sodium acetate Resolution 2.95 Å R-free 0.242

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 6m58

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6m58
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6m58
Deposition date deposition_date2020-03-10
Structure title titleCrystal structure of a complex between human serum albumin and the antibody Fab SL335
Keywords keywordsSERUM ALBUMIN, ANTI-ALBUMIN, ANTIBODY FAB, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.32
Radius of gyration Rg (electron density) rg_electron43.06
Forward intensity I(0) i0660898000.00
Molecular weight molecular_weight209440.0 kDa
Excluded volume excluded_volume261000 ų
Envelope volume envelope_volume357430 ų
Hydration-shell volume shell_volume69075 ų
Envelope diameter envelope_diameter159.1
Shell Rg shell_rg47.89
Envelope Rg envelope_rg43.02
Shape Rg shape_rg43.07
Total Rg total_rg43.25
Total atoms total_atoms14723
Residues n_residues1940
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 dmax148.5
Rg (real space) rg_real43.35
Rg uncertainty (real space) rg_real_error1.34
I(0) (real space) i0_real6.6090e+08
I(0) uncertainty (real space) i0_real_error1.2080e+07
Rg (reciprocal space) rg_reciprocal43.32
I(0) (reciprocal space) i0_reciprocal660900000.0000
Solution quality estimate total_estimate0.8762
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.5
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.217
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha105500000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id6m58A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m58A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m58A03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m58B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m58C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6m58C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6m58D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6m58D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6m58H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6m58H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6m58L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6m58L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)