SAXSdb — 2p63

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

Cell division control protein 4

Saccharomyces cerevisiae

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 222–273 Chain B； UniProt 222–273 Chain C； UniProt 222–273 Chain D； UniProt 222–273	Fragment：D Domain Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；50%MPD, 100 mM (NH4)H2PO4 ph 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.67 Å R-free 0.279
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 222–273 Chain D； UniProt 222–273	Fragment：D Domain Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；50%MPD, 100 mM (NH4)H2PO4 ph 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.67 Å R-free 0.279
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 222–273 Chain B； UniProt 222–273	Fragment：D Domain Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；50%MPD, 100 mM (NH4)H2PO4 ph 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.67 Å R-free 0.279

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.

Other PDB	Difference from Current Entry 2P63	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NEX Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex Deposited 2002-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 263–744（482 aa） Fragment：residues 601-604 and 609-624 deleted	Mutation：C608L Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Ammonium Sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.273
1NEX Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex Deposited 2002-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 263–744（482 aa） Fragment：residues 601-604 and 609-624 deleted	Mutation：C608L Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Ammonium Sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.273
3MKS Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 Deposited 2010-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 263–744（482 aa） Fragment：UNP Residues 263-744 with 602-605 and 609-624 deleted Chain D 263–744（482 aa） Fragment：UNP Residues 263-744 with 602-605 and 609-624 deleted	Not recorded	SO4 SULFATE ION × 11 C1C 1,1'-binaphthalene-2,2'-dicarboxylic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.266
3MKS Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 Deposited 2010-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 263–744（482 aa） Fragment：UNP Residues 263-744 with 602-605 and 609-624 deleted	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.266
3MKS Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 Deposited 2010-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 263–744（482 aa） Fragment：UNP Residues 263-744 with 602-605 and 609-624 deleted	Not recorded	SO4 SULFATE ION × 6 C1C 1,1'-binaphthalene-2,2'-dicarboxylic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.266
3V7D Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex Deposited 2011-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 263–744（482 aa） Fragment：UNP residues 263-744	Mutation：C608L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammonium Sulphate, 0.1 M Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.31 Å R-free 0.221
3V7D Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex Deposited 2011-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 263–744（482 aa） Fragment：UNP residues 263-744	Mutation：C608L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammonium Sulphate, 0.1 M Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.31 Å R-free 0.221

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDC4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–56； UniProt 222–273 Author chain B； PDBConstruct 5–56； UniProt 222–273 Author chain C； PDBConstruct 5–56； UniProt 222–273 Author chain D； PDBConstruct 5–56； UniProt 222–273

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2p63
Deposition date deposition_date	2007-03-16
Structure title title	Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination
Keywords keywords	ubiquitination, helix bundle, scf complex, CELL CYCLE; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.62 Å
Radius of gyration Rg (electron density) rg_electron	19.61 Å
Forward intensity I(0) i0	10624900.00
Molecular weight molecular_weight	23966.0 kDa
Excluded volume excluded_volume	29917 Å³
Envelope volume envelope_volume	37922 Å³
Hydration-shell volume shell_volume	16968 Å³
Envelope diameter envelope_diameter	76.8 Å
Shell Rg shell_rg	24.79 Å
Envelope Rg envelope_rg	19.75 Å
Shape Rg shape_rg	19.64 Å
Total Rg total_rg	20.34 Å
Total atoms total_atoms	1678
Residues n_residues	203
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/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	72.5 Å
Rg (real space) rg_real	20.60 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	1.0620e+07
I(0) uncertainty (real space) i0_real_error	1.6010e+05
Rg (reciprocal space) rg_reciprocal	20.60 Å
I(0) (reciprocal space) i0_reciprocal	10620000.0000
Solution quality estimate total_estimate	0.7756
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.343
Kurtosis Kurtosis kurtosis	-0.105
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1238000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2p63A01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — Cdc4 dimerisation domain-like

Domain ID domain_id	2p63B01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — Cdc4 dimerisation domain-like

Domain ID domain_id	2p63C01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — Cdc4 dimerisation domain-like

Domain ID domain_id	2p63D01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — Cdc4 dimerisation domain-like

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8. Citations (1)

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Unit-cell length a length_a	37.816 Å
Unit-cell length b length_b	37.816 Å
Unit-cell length c length_c	298.118 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.670 Å
Low-resolution limit resolution_low	49.690 Å
R factor r_factor	0.2240
R_work r_work	0.2197
R_free r_free	0.2785

Description description	Cell division control protein 4
Molecular weight formula_weight	6429.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1742

Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination

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

Cell division control protein 4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

fit	/app/data/saxs_computation/p6/2p63/2p63.fit
pddf	/app/data/pr_computation/p6/2p63/2p63.pr.out
profile	/app/data/saxs_computation/p6/2p63/2p63.dat