6o8d

Anti-CD28xCD3 CODV Fab bound to CD28

Method: X-RAY DIFFRACTION Dmax: 116.3 Å Quality: GOOD

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

T-cell-specific surface glycoprotein CD28

Homo sapiens

UniProt P10747

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 2 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 33–150 Not recorded Anti-CD28xCD3 CODV Fab Light chain × 2 Anti-CD28xCD3 CODV Fab Heavy chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;26% PEG3350, 0.75% myo-inositol, 0.263M potassium citrate tribasic monohydrate Resolution 3.55 Å R-free 0.356

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.

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

View Construct and Data Evidence
UniProt name CD28_HUMAN
Isoform P10747-7
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 1–118; UniProt 33–150

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 6o8d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6o8d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6o8d
Deposition date deposition_date2019-03-09
Structure title titleAnti-CD28xCD3 CODV Fab bound to CD28
Keywords keywords;Multispecific antibody, cross-over dual variable immunoglobin, multifunctional biotherapeutic format, bispecific property, CODV, immune system, T cell activation ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.80
Radius of gyration Rg (electron density) rg_electron35.42
Forward intensity I(0) i0121666000.00
Molecular weight molecular_weight87762.0 kDa
Excluded volume excluded_volume109650 ų
Envelope volume envelope_volume157300 ų
Hydration-shell volume shell_volume38042 ų
Envelope diameter envelope_diameter122.4
Shell Rg shell_rg40.84
Envelope Rg envelope_rg34.38
Shape Rg shape_rg35.38
Total Rg total_rg35.96
Total atoms total_atoms6183
Residues n_residues796
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 dmax116.3
Rg (real space) rg_real35.79
Rg uncertainty (real space) rg_real_error0.91
I(0) (real space) i0_real1.2170e+08
I(0) uncertainty (real space) i0_real_error1.9570e+06
Rg (reciprocal space) rg_reciprocal35.80
I(0) (reciprocal space) i0_reciprocal121700000.0000
Solution quality estimate total_estimate0.8827
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.2
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.593
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17060000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.752

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id6o8dC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o8dH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o8dH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o8dH03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o8dL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o8dL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o8dL03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)