5vnw

Crystal structure of Nb.b201 bound to human serum albumin

Method: X-RAY DIFFRACTION Dmax: 181.3 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 25–609 Not recorded Nb.b201 × 1 GOL GLYCEROL × 3 PLM PALMITIC ACID × 1 DAO LAURIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, Tris(base)/BICINE pH 8.5, PEG 500 MME, PEG 20,0000, sodium chloride, HEPES pH 7.5 Resolution 2.60 Å R-free 0.256
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 25–609 Not recorded Nb.b201 × 1 GOL GLYCEROL × 1 PLM PALMITIC ACID × 1 BUA butanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, Tris(base)/BICINE pH 8.5, PEG 500 MME, PEG 20,0000, sodium chloride, HEPES pH 7.5 Resolution 2.60 Å R-free 0.256

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 5vnw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vnw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5vnw
Deposition date deposition_date2017-05-01
Structure title titleCrystal structure of Nb.b201 bound to human serum albumin
Keywords keywordsnanobody, synthetic protein, llama, camelid, TRANSPORT PROTEIN-DE NOVO PROTEIN complex; TRANSPORT PROTEIN/DE NOVO PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier56.71
Radius of gyration Rg (electron density) rg_electron57.37
Forward intensity I(0) i0369254000.00
Molecular weight molecular_weight157930.0 kDa
Excluded volume excluded_volume196790 ų
Envelope volume envelope_volume309530 ų
Hydration-shell volume shell_volume49003 ų
Envelope diameter envelope_diameter190.5
Shell Rg shell_rg52.50
Envelope Rg envelope_rg55.24
Shape Rg shape_rg57.35
Total Rg total_rg57.28
Total atoms total_atoms11071
Residues n_residues1404
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 dmax181.3
Rg (real space) rg_real57.35
Rg uncertainty (real space) rg_real_error1.90
I(0) (real space) i0_real3.6930e+08
I(0) uncertainty (real space) i0_real_error8.3560e+06
Rg (reciprocal space) rg_reciprocal56.11
I(0) (reciprocal space) i0_reciprocal368500000.0000
Solution quality estimate total_estimate0.5244
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9
Skewness Skewness skewness0.432
Kurtosis Kurtosis kurtosis-0.794
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16880000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 0.003; Positv: 1.000; Valcen: 0.590; Smooth: 0.005

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id5vnwA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwA06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwB04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwB05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id5vnwB06
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)