SAXSdb — 2p64

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

F-box/WD repeat protein 1A

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 128–177 Chain B； UniProt 128–177	Fragment：D domain Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；200 mM MgCl2, 5 mM CdCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.267

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 2P64	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1P22 Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity on the SCFbeta-TrCP1 ubiquitin ligase Deposited 2003-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–605（431 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG4000, sodium citrate, Bis-Tris Propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.95 Å R-free 0.286
6M90 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–605（431 aa）	Not recorded	J91 2-(2-fluorophenoxy)-3-{[2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.05 Å R-free 0.212
6M91 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–605（431 aa）	Not recorded	J97 3-({4-[(2,6-dichlorophenyl)sulfanyl]-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl}amino)benzoic acid × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.40 Å R-free 0.216
6M92 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–605（431 aa）	Not recorded	J8V 3-{[2-oxo-4-phenoxy-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.35 Å R-free 0.221
6M93 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–605（431 aa）	Not recorded	J8Y 2-oxo-N-[3-(1H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.50 Å R-free 0.230
6M94 Monophosphorylated pSer33 b-Catenin peptide bound to b-TrCP/Skp1 Complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–605（431 aa）	Not recorded	PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH5.5	Resolution 2.70 Å R-free 0.238
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30	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 × 8 PDB declaration: octameric	Chain T 1–605（605 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9T8Y Crystal structure of beta-TrCP bound by monophosphorylated NRF2 degron peptide. Deposited 2025-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 222–584（363 aa）	Mutation：L188E, L192E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；19% PEG3350, 0.1 M PCTP pH 6.2	Resolution 1.79 Å R-free 0.265
9T95 Crystal structure of beta-TrCP bound by diphosphorylated NRF2 degron peptide. Deposited 2025-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 222–584（363 aa）	Mutation：L188E, L192E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.1 M Na HEPES pH 7.5	Resolution 2.15 Å R-free 0.277
9T9W Crystal structure of beta-TrCP bound by diphosphorylated I-kappa-B-alpha degron peptide Deposited 2025-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 222–584（363 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；18% PEG8K	Resolution 1.16 Å R-free 0.213
9TDZ Crystal structure of beta-TrCP bound by diphosphorylated claspin degron peptide Deposited 2025-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 222–584（363 aa）	Mutation：L188E, L192E	EDO 1,2-ETHANEDIOL × 8 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG4K, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6	Resolution 1.35 Å R-free 0.204
9TES Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide Deposited 2025-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 222–584（363 aa）	Mutation：L188E, L192E	MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG10K, 0.1 M Na-Hepes pH 7.5	Resolution 1.22 Å R-free 0.240
9TFU Crystal structure of beta-TrCP bound by monophosphorylated ATF4 degron peptide Deposited 2025-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 222–584（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEGMME2K, 0.1 M Bis-tris pH 6.5	Resolution 2.00 Å R-free 0.236
9TG7 Crystal structure of beta-TrCP bound by monophosphorylated WEE1 degron peptide Deposited 2025-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 222–584（363 aa）	Mutation：L188E, L192E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；20% PEG10K, 0.1 M Na-Hepes pH 7.5	Resolution 1.68 Å R-free 0.252

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FBW1A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–52； UniProt 128–177 Author chain B； PDBConstruct 3–52； UniProt 128–177

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	2p64
Deposition date deposition_date	2007-03-16
Structure title title	D domain of b-TrCP
Keywords keywords	right handed super-helical bundle, LIGASE; LIGASE
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	14.43 Å
Radius of gyration Rg (electron density) rg_electron	13.22 Å
Forward intensity I(0) i0	3559850.00
Molecular weight molecular_weight	12645.0 kDa
Excluded volume excluded_volume	15399 Å³
Envelope volume envelope_volume	17221 Å³
Hydration-shell volume shell_volume	11122 Å³
Envelope diameter envelope_diameter	45.2 Å
Shell Rg shell_rg	18.96 Å
Envelope Rg envelope_rg	13.69 Å
Shape Rg shape_rg	13.22 Å
Total Rg total_rg	14.43 Å
Total atoms total_atoms	869
Residues n_residues	99
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	46.9 Å
Rg (real space) rg_real	14.34 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	3.5600e+06
I(0) uncertainty (real space) i0_real_error	3.5420e+04
Rg (reciprocal space) rg_reciprocal	14.35 Å
I(0) (reciprocal space) i0_reciprocal	3560000.0000
Solution quality estimate total_estimate	0.8737
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.6 Å
Skewness Skewness skewness	0.143
Kurtosis Kurtosis kurtosis	-0.307
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	653700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	F-box/WD repeat protein 1A
Molecular weight formula_weight	6321.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	890

GAASYEKEKELCVKYFEQWSESDQVEFVEHLISQMCHYQHGHINSYLKPMLQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2p64A00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1840 —

Domain ID domain_id	2p64B00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1840 —

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8. Citations (1)

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Unit-cell length a length_a	71.316 Å
Unit-cell length b length_b	71.316 Å
Unit-cell length c length_c	116.301 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.780 Å
R factor r_factor	0.2399
R_work r_work	0.2385
R_free r_free	0.2668

fit	/app/data/saxs_computation/p6/2p64/2p64.fit
pddf	/app/data/pr_computation/p6/2p64/2p64.pr.out
profile	/app/data/saxs_computation/p6/2p64/2p64.dat

D domain of b-TrCP

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

F-box/WD repeat protein 1A

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