9y59
Crystal structure of CSD20f3B, a designed switching binder to CSD20f3A
1. Protein Identity and Related Structures Protein Identity & Related Structures
No usable UniProt protein identity is available for this entry.
七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。
Assembly Composition of the Current Entry
| Assembly | Oligomeric State | 实体与Construct证据 | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
| 2 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
| 3 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
| 4 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
| 5 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
| 6 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
| 7 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
| 8 | Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric | Entity 1：CSD20f3B × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium sulfate, 0.3 M Sodium formate, 0.1 M Tris pH 7.8, 3 % (w/v) gamma-PGA (Na+ form, LM) and 5 % (w/v) PEG 4000 | Resolution 3.87 Å R-free 0.282 |
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
P(r) Distance Distribution P(r) Distribution
2. Structure Basics 2. Structure Basics
| Entry ID entry_id | 9y59 |
| Deposition date deposition_date | 2025-09-04 |
| 最后修订 last_revision | 2025-09-17 |
| Structure title title | Crystal structure of CSD20f3B, a designed switching binder to CSD20f3A |
| Keywords keywords | de novo protein, design model, Effector, kinetics and dynamics, Protein-protein interactions; DE NOVO PROTEIN |
| Experimental Method method | X-RAY DIFFRACTION |
3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)
| Radius of gyration Rg (Guinier) rg_guinier | 37.14 Å |
| Radius of gyration Rg (electron density) rg_electron | 36.47 Å |
| Forward intensity I(0) i0 | 369623000.00 |
| Molecular weight molecular_weight | 147590.0 kDa |
| Excluded volume excluded_volume | 182510 ų |
| Envelope volume envelope_volume | 236910 ų |
| Hydration-shell volume shell_volume | 53984 ų |
| Envelope diameter envelope_diameter | 124.4 Å |
| Shell Rg shell_rg | 42.63 Å |
| Envelope Rg envelope_rg | 36.29 Å |
| Shape Rg shape_rg | 36.47 Å |
| Total Rg total_rg | 36.85 Å |
| Total atoms total_atoms | 10366 |
| Residues n_residues | 1310 |
| Spherical-harmonic order n_harmonics | 20 |
| q range q_range | — – 0.5000 Å−1 |
| Data points n_points | 101 |
| Shell type shell_type | directional |
| Solvent electron density solvent_density | 0.3340 e/ų |
| Shell contrast contrast_shell | 0.0300 e/ų |
| CRYSOL version crysol_version | 4.1.3 |
4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)
| Maximum dimension Dmax dmax | 119.3 Å |
| Rg (real space) rg_real | 37.06 Å |
| Rg uncertainty (real space) rg_real_error | 0.71 Å |
| I(0) (real space) i0_real | 3.6960e+08 |
| I(0) uncertainty (real space) i0_real_error | 5.3970e+06 |
| Rg (reciprocal space) rg_reciprocal | 37.12 Å |
| I(0) (reciprocal space) i0_reciprocal | 369600000.0000 |
| Solution quality estimate total_estimate | 0.8962 |
| Solution quality rating solution_quality | GOOD a GOOD solution |
| P(r) peaks n_peaks | 1 |
| Primary peak position r_peak_primary | 44.4 Å |
| Skewness Skewness skewness | 0.259 |
| Kurtosis Kurtosis kurtosis | -0.469 |
| Angular range angular_range | — – 0.2150 Å−1 |
| Current regularization parameter α current_alpha | 0.0001 |
| Highest regularization parameter α highest_alpha | 134400000.0000 |
| Real-space data points n_real_points | 44 |
| GNOM version gnom_version | 4.1.3 |
| Quality Criteria quality_criteria | AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.883 |