4qti

Crystal structure of human uPAR in complex with anti-uPAR Fab 8B12

Method: X-RAY DIFFRACTION Dmax: 124.0 Å Quality: GOOD

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

Urokinase plasminogen activator surface receptor

Homo sapiens

UniProt Q03405

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 U; UniProt 23–305 Not recorded anti-uPAR antibody, heavy chain × 1 anti-uPAR antibody, light chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;48% MPD, 100mM Tris, 100mM NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.00 Å R-free 0.296

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 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UPAR_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain U; PDBConstruct 1–283; UniProt 23–305

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 4qti

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qti
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qti
Deposition date deposition_date2014-07-08
Structure title titleCrystal structure of human uPAR in complex with anti-uPAR Fab 8B12
Keywords keywordsallosteric regulation, cell surface, 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_guinier35.68
Radius of gyration Rg (electron density) rg_electron35.69
Forward intensity I(0) i0101821000.00
Molecular weight molecular_weight75732.0 kDa
Excluded volume excluded_volume92697 ų
Envelope volume envelope_volume128930 ų
Hydration-shell volume shell_volume33155 ų
Envelope diameter envelope_diameter127.7
Shell Rg shell_rg38.13
Envelope Rg envelope_rg35.54
Shape Rg shape_rg35.66
Total Rg total_rg35.97
Total atoms total_atoms5290
Residues n_residues690
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 dmax124.0
Rg (real space) rg_real36.08
Rg uncertainty (real space) rg_real_error1.65
I(0) (real space) i0_real1.0180e+08
I(0) uncertainty (real space) i0_real_error1.7590e+06
Rg (reciprocal space) rg_reciprocal35.83
I(0) (reciprocal space) i0_reciprocal101800000.0000
Solution quality estimate total_estimate0.8146
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.8
Skewness Skewness skewness0.542
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6334000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.634; Smooth: 0.815

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd4qtih1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4qtih2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4qtil1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4qtil2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd4qtiu1
Class classg — Small proteins
Fold Fold foldg.7 — Snake toxin-like
Superfamily Superfamily superfamilyg.7.1 — Snake toxin-like
Family Family familyg.7.1.3 — Extracellular domain of cell surface receptors
Domain ID domain_idd4qtiu2
Class classg — Small proteins
Fold Fold foldg.7 — Snake toxin-like
Superfamily Superfamily superfamilyg.7.1 — Snake toxin-like
Family Family familyg.7.1.3 — Extracellular domain of cell surface receptors
Domain ID domain_idd4qtiu3
Class classg — Small proteins
Fold Fold foldg.7 — Snake toxin-like
Superfamily Superfamily superfamilyg.7.1 — Snake toxin-like
Family Family familyg.7.1.3 — Extracellular domain of cell surface receptors

CATH v4.4 (7 domains)

Domain ID domain_id4qtiH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qtiH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qtiL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qtiL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qtiU01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59
Domain ID domain_id4qtiU02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59
Domain ID domain_id4qtiU03
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59

8. Citations (1)

9. Files and Curves (10)