8y9s

Crystal structure of nanobody MY6321 bound to human serum albumin (HSA)

Method: X-RAY DIFFRACTION Dmax: 117.8 Å Quality: EXCELLENT

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

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 19–609 Not recorded nanobody MY6321 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;0.15 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350 Resolution 2.88 Å R-free 0.293
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 19–609 Not recorded nanobody MY6321 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;0.15 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350 Resolution 2.88 Å R-free 0.293

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 1–591; UniProt 19–609 Author chain C; PDBConstruct 1–591; UniProt 19–609

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 8y9s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8y9s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8y9s
Deposition date deposition_date2024-02-07
Structure title titleCrystal structure of nanobody MY6321 bound to human serum albumin (HSA)
Keywords keywordsantibody, human serum albumin, 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_guinier37.97
Radius of gyration Rg (electron density) rg_electron37.21
Forward intensity I(0) i0374117000.00
Molecular weight molecular_weight155650.0 kDa
Excluded volume excluded_volume194290 ų
Envelope volume envelope_volume265040 ų
Hydration-shell volume shell_volume58751 ų
Envelope diameter envelope_diameter122.0
Shell Rg shell_rg44.15
Envelope Rg envelope_rg36.46
Shape Rg shape_rg37.20
Total Rg total_rg37.69
Total atoms total_atoms10901
Residues n_residues1382
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 dmax117.8
Rg (real space) rg_real37.78
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real3.7410e+08
I(0) uncertainty (real space) i0_real_error5.6990e+06
Rg (reciprocal space) rg_reciprocal37.91
I(0) (reciprocal space) i0_reciprocal374200000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.7
Skewness Skewness skewness0.165
Kurtosis Kurtosis kurtosis-0.513
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40860000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.883

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)