SAXSdb — 2kdi

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

Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein

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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–76	Fragment：UIM 1	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 0.103；Pressure ambient NMR sample composition：1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.5 mM [U-100% 15N] Ubiquitin/UIM fusion protein-9, 3 mM sodium azide-10, 20 mM sodium phosphate-11, 50 mM sodium chloride-12, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	B3LRG8_YEAS1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–85； UniProt 2–76

Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein

Saccharomyces cerevisiae

UniProt P40343

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 258–277	Fragment：UIM 1	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 0.103；Pressure ambient NMR sample composition：1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.5 mM [U-100% 15N] Ubiquitin/UIM fusion protein-9, 3 mM sodium azide-10, 20 mM sodium phosphate-11, 50 mM sodium chloride-12, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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 2KDI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1Q0V Solution Structure of Tandem UIMs of Vps27 Deposited 2003-07-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–329（81 aa） Fragment：Tandem UIM	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM Vps27 UIM U-15N \| 90% H2O/10% D2O NMR sample composition 1 mM Vps27 UIM U-15N,U-13C \| 100% D2O	Resolution not provided
1Q0W Solution structure of Vps27 amino-terminal UIM-ubiquitin complex Deposited 2003-07-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 256–279（24 aa） Fragment：Amino-terminal UIM, residues 256 to 278	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 100% D2O	Resolution not provided
1VFY PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PROTEIN FROM SACCHAROMYCES CEREVISIAE Deposited 1999-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 163–230（68 aa） Fragment：163-229, FYVE DOMAIN	Mutation：6 RESIDUES (EFIVTD) INSERTED AT C-TERMINUS	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.6, 15% PEG 4000, pH 5.6	Resolution 1.15 Å R-free 0.181
2PJW The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting Deposited 2007-04-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain V 348–438（91 aa）	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, SITTING DROP；pH 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285
2PJW The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting Deposited 2007-04-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 348–438（91 aa）	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, SITTING DROP；pH 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 445–453（9 aa） Fragment：PSDP peptide (UNP residues 445-453)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；288 K；0.2 M sodium phosphate monobasic, 20% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.87 Å R-free 0.203
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 445–453（9 aa） Fragment：PSDP peptide (UNP residues 445-453)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；288 K；0.2 M sodium phosphate monobasic, 20% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.87 Å R-free 0.203
6NJG Ubiquitin Variant in Complex with Ubiquitin Interacting Motif Deposited 2019-01-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 256–278（23 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid	Resolution 2.35 Å R-free 0.244

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS27_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 92–111； UniProt 258–277

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	2kdi
Deposition date deposition_date	2009-01-09
Structure title title	Solution structure of a Ubiquitin/UIM fusion protein
Keywords keywords	;Ubiquitin, Ubiquitin Interacting Motif, UIM, protein domain interface, Endosome, Membrane, Metal-binding, Phosphoprotein, Zinc, Zinc-finger, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.97 Å
Radius of gyration Rg (electron density) rg_electron	15.13 Å
Forward intensity I(0) i0	1013690000.00
Molecular weight molecular_weight	256850.0 kDa
Excluded volume excluded_volume	316970 Å³
Envelope volume envelope_volume	50106 Å³
Hydration-shell volume shell_volume	20319 Å³
Envelope diameter envelope_diameter	70.3 Å
Shell Rg shell_rg	27.92 Å
Envelope Rg envelope_rg	22.06 Å
Shape Rg shape_rg	15.14 Å
Total Rg total_rg	15.39 Å
Total atoms total_atoms	35960
Residues n_residues	2280
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	62.8 Å
Rg (real space) rg_real	16.05 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.0140e+09
I(0) uncertainty (real space) i0_real_error	1.4010e+07
Rg (reciprocal space) rg_reciprocal	16.04 Å
I(0) (reciprocal space) i0_reciprocal	1014000000.0000
Solution quality estimate total_estimate	0.7645
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.3 Å
Skewness Skewness skewness	0.552
Kurtosis Kurtosis kurtosis	0.306
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	446600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.423; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.672; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2kdiA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (2)

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Description description	Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein
Molecular weight formula_weight	12867.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	35960

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/kd/2kdi/2kdi.fit
pddf	/app/data/pr_computation/kd/2kdi/2kdi.pr.out
profile	/app/data/saxs_computation/kd/2kdi/2kdi.dat

Solution structure of a Ubiquitin/UIM fusion protein

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

Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)