SAXSdb — 1nex

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

Centromere DNA-binding protein complex CBF3 subunit D

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–193	Fragment：residues 36-63 deleted Non-standard monomer：Yes (specific site not provided by mmCIF)	CDC4 protein × 1 （P07834） GLL(TPO)PPQSG × 1	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–193	Fragment：residues 36-63 deleted Non-standard monomer：Yes (specific site not provided by mmCIF)	CDC4 protein × 1 （P07834） GLL(TPO)PPQSG × 1	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

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 1NEX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 A 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 deleted Chain C 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 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 A 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 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 C 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–194（194 aa）	Not recorded	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 C 1–194（194 aa）	Not recorded	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
5AN3 Structure of an Sgt1-Skp1 Complex Deposited 2015-09-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–35（35 aa） Fragment：BTBPOZ DOMAIN, UNP RESIDUES 1-35,65-158 Chain D 65–158（94 aa） Fragment：BTBPOZ DOMAIN, UNP RESIDUES 1-35,65-158	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.325 M MGCL2, 22.5% PEG-6000, 0.1 M TRIS-HCL PH 8	Resolution 2.82 Å R-free 0.241
6F07 CBF3 Core Complex Deposited 2017-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–194（194 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6FE8 Cryo-EM structure of the core Centromere Binding Factor 3 complex Deposited 2017-12-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–194（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6GSA Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Deposited 2018-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: tetrameric	Chain C 2–194（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GYP Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–194（194 aa）	Not recorded	MET METHIONINE × 1 PHE PHENYLALANINE × 1 ASN ASPARAGINE × 1 ARG ARGININE × 1 THR THREONINE × 2 GLN GLUTAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GYS Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain D 1–194（194 aa） Chain K 1–194（194 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
6GYU Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore Deposited 2018-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–194（194 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7K79 CBF3 Deposited 2020-09-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 1–194（194 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7PMN S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II) Deposited 2021-09-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain K 1–194（194 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger	Resolution 3.20 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain SK 1–194（194 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain z 1–194（194 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SKP1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–169； UniProt 1–193 Author chain C； PDBConstruct 4–169； UniProt 1–193

CDC4 protein

Saccharomyces cerevisiae

UniProt P07834

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 B； UniProt 263–744	Fragment：residues 601-604 and 609-624 deleted Mutation：C608L Non-standard monomer：Yes (specific site not provided by mmCIF)	Centromere DNA-binding protein complex CBF3 subunit D × 1 （P52286） GLL(TPO)PPQSG × 1	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 263–744	Fragment：residues 601-604 and 609-624 deleted Mutation：C608L Non-standard monomer：Yes (specific site not provided by mmCIF)	Centromere DNA-binding protein complex CBF3 subunit D × 1 （P52286） GLL(TPO)PPQSG × 1	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

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 1NEX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2P63 Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination Deposited 2007-03-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 222–273（52 aa） Fragment：D Domain Chain B 222–273（52 aa） Fragment：D Domain Chain C 222–273（52 aa） Fragment：D Domain Chain D 222–273（52 aa） Fragment：D Domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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 8.5；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
2P63 Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination Deposited 2007-03-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 222–273（52 aa） Fragment：D Domain Chain D 222–273（52 aa） Fragment：D Domain	Non-standard monomer：Yes (specific site not provided by mmCIF) 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 8.5；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
2P63 Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination Deposited 2007-03-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 222–273（52 aa） Fragment：D Domain Chain B 222–273（52 aa） Fragment：D Domain	Non-standard monomer：Yes (specific site not provided by mmCIF) 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 8.5；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
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 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 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDC4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–464； UniProt 263–744 Author chain D； PDBConstruct 3–464； UniProt 263–744

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	1nex
Deposition date deposition_date	2002-12-12
Structure title title	Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex
Keywords keywords	WD 40 domain, phospho-peptide complex, E3 ubiquitin ligase, LIGASE, CELL CYCLE; LIGASE, 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	44.35 Å
Radius of gyration Rg (electron density) rg_electron	43.95 Å
Forward intensity I(0) i0	259410000.00
Molecular weight molecular_weight	133590.0 kDa
Excluded volume excluded_volume	167640 Å³
Envelope volume envelope_volume	238070 Å³
Hydration-shell volume shell_volume	46794 Å³
Envelope diameter envelope_diameter	138.0 Å
Shell Rg shell_rg	47.19 Å
Envelope Rg envelope_rg	42.29 Å
Shape Rg shape_rg	43.91 Å
Total Rg total_rg	44.24 Å
Total atoms total_atoms	9363
Residues n_residues	1139
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	139.7 Å
Rg (real space) rg_real	44.45 Å
Rg uncertainty (real space) rg_real_error	1.28 Å
I(0) (real space) i0_real	2.5940e+08
I(0) uncertainty (real space) i0_real_error	4.5390e+06
Rg (reciprocal space) rg_reciprocal	44.35 Å
I(0) (reciprocal space) i0_reciprocal	259400000.0000
Solution quality estimate total_estimate	0.8302
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.8 Å
Skewness Skewness skewness	0.233
Kurtosis Kurtosis kurtosis	-0.761
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16830000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Centromere DNA-binding protein complex CBF3 subunit D
Molecular weight formula_weight	19739.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	9435

GAHMVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

来源 Source

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

Entity 2 Entity 2 polymer

Description description	CDC4 protein
Molecular weight formula_weight	53143.5 kDa
Mutation mutation	C608L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GAGTLIKDNLKRDLITSLPFEISLKIFNYLQFEDIINSLGVSQNWNKIIRKSTSLWKKLLISENFVSPKGFNSLNLKLSQKYPKLSQQDRLRLSFLENIFILKNWYNPKFVPQRTTLRGHMTSVITCLQFEDNYVITGADDKMIRVYDSINKKFLLQLSGHDGGVWALKYAHGGILVSGSTDRTVRVWDIKKGCCTHVFEGHNSTVRCLDIVEYKNIKYIVTGSRDNTLHVWKLPKESSVPDHGEEHDYPLVFHTPEENPYFVGVLRGHMASVRTVSGHGNIVVSGSYDNTLIVWDVAQMKCLYILSGHTDRIYSTIYDHERKRCISASMDTTIRIWDLENGELMYTLQGHTALVGLLRLSDKFLVSAAADGSIRGWDANDYSRKFSYHHTNLSAITTFYVSDNILVSGSENQFNIYNLRSGKLVHANILKDADQIWSVNFKGKTLVAAVEKDGQSFLEILDFS

来源 Source

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

Entity 3 Entity 3 polymer

Description description	GLL(TPO)PPQSG
Molecular weight formula_weight	949.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

GLLTPPQSG

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1nexa1
Class class	a — All alpha proteins
Fold Fold fold	a.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
Family Family family	a.157.1.1 — Skp1 dimerisation domain-like

Domain ID domain_id	d1nexa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d1nexb1
Class class	a — All alpha proteins
Fold Fold fold	a.158 — F-box domain
Superfamily Superfamily superfamily	a.158.1 — F-box domain
Family Family family	a.158.1.1 — F-box domain

Domain ID domain_id	d1nexb2
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1nexc1
Class class	a — All alpha proteins
Fold Fold fold	a.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
Family Family family	a.157.1.1 — Skp1 dimerisation domain-like

Domain ID domain_id	d1nexc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d1nexd1
Class class	a — All alpha proteins
Fold Fold fold	a.158 — F-box domain
Superfamily Superfamily superfamily	a.158.1 — F-box domain
Family Family family	a.158.1.1 — F-box domain

Domain ID domain_id	d1nexd2
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

CATH v4.4 (6 domains)

Domain ID domain_id	1nexA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	1nexB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1nexB02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1nexC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	1nexD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1nexD02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	107.669 Å
Unit-cell length b length_b	107.669 Å
Unit-cell length c length_c	168.300 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	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2730

fit	/app/data/saxs_computation/ne/1nex/1nex.fit
pddf	/app/data/pr_computation/ne/1nex/1nex.pr.out
profile	/app/data/saxs_computation/ne/1nex/1nex.dat

Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex

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

Centromere DNA-binding protein complex CBF3 subunit D

State in the Current Structure

Other States of the Same Protein in the Database

CDC4 protein

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)