SAXSdb — 1ywi

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

Formin-binding protein 3

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 142–173	Fragment：WW1 domain	Formin × 1	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition：1.8mM [U-15N,13C] FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 90% H2O/10% D2O NMR sample composition：1.8mM [U-15N,13C] FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 100% D2O NMR sample composition：1.8mM [U-15N] FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 90% H2O/10% D2O NMR sample composition：1.8mM FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 90% H2O/10% 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 1YWI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YWJ Structure of the FBP11WW1 domain Deposited 2005-02-18	Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 142–173（32 aa） Fragment：WW1 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition 1.8mM [U-15N,13C] FBP11WW1, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 90% H2O/10% D2O NMR sample composition 1.8mM [U-15N,13C] FBP11WW1, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 100% D2O NMR sample composition 1.8mM [U-15N] FBP11WW1, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 90% H2O/10% D2O NMR sample composition 1.8mM FBP11WW1, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA \| 90% H2O/10% D2O	Resolution not provided
2CQN Solution structure of the FF domain of human Formin-binding protein 3 Deposited 2005-05-20	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 743–806（64 aa） Fragment：FF domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.9mM 13C/15N-PROTEIN; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2DYF Solution structure of the first WW domain of FBP11 / HYPA (FBP11 WW1) complexed with a PL (PPLP) motif peptide ligand Deposited 2006-09-11	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 146–173（28 aa） Fragment：THE FIRST WW DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；283 K；Ionic strength (raw mmCIF value) 0.3；Pressure 1 NMR sample composition 1.5MM FBP11 WW1 U-15N, 13C 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.5MM FBP11 WW1 U- 15N, 13C; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.5MM FBP11 WW1 U-15N; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O	Resolution not provided
2KZG A Transient and Low Populated Protein Folding Intermediate at Atomic Resolution Deposited 2010-06-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–450（70 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.7；303 K；Ionic strength (raw mmCIF value) 145；Pressure ambient NMR sample composition 1-2 mM [U-13C; U-15N; U-2H] FF-1, 100 mM sodium chloride-2, 50 mM sodium acetate-3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1-2 mM [U-100% 13C; U-100% 15N; U-50% 2H] FF-4, 100 mM sodium chloride-5, 50 mM sodium acetate-6, 100% D2O \| 100% D2O NMR sample composition 1-2 mM [selective 13C; U-100% 15N] FF-7, 100 mM sodium chloride-8, 50 mM sodium acetate-9, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L5F Solution structure of the tandem WW domains from HYPA/FBP11 Deposited 2010-11-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 133–220（88 aa） Fragment：WW domains (UNP RESIDUES 133-220)	Mutation：P67T	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient NMR sample composition 10 mM sodium phosphate-1, 100 mM sodium chloride-2, 5 mM DTT-3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L9V NMR structure of the FF domain L24A mutant's folding transition state Deposited 2011-02-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–450（70 aa） Fragment：FF 1 domain residues 390-438	Mutation：L24A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.7；303 K；Ionic strength (raw mmCIF value) 145；Pressure ambient NMR sample composition 1-2 mM [U-13C; U-15N; U-2H] protein, 100 mM sodium chloride, 50 mM sodium acetate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1-2 mM [U-100% 13C; U-100% 15N; U-50% 2H] protein, 100 mM sodium chloride, 50 mM sodium acetate, 100% D2O \| 100% D2O	Resolution not provided
2LKS Ff11-60 Deposited 2011-10-19	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–439（49 aa） Fragment：FF 1 domain residues 391-439	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；298 K；Ionic strength (raw mmCIF value) 0.070；Pressure ambient NMR sample composition 20 mM sodium acetate, 50 mM sodium chloride, 0.05 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] FF11, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 20 mM sodium acetate, 50 mM sodium chloride, 0.05 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] FF11-60 A51L, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 20 mM 20mM sodium acetate, 50 mM 50 mM sodium chloride, 0.05 % 0.05% sodium azide, 1 mM [U-10% 13C; U-100% 15N] FF11, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
8PXW Structure of the WW domain tandem of PRPF40A Deposited 2023-07-24	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 141–236（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 133；Pressure 1 NMR sample composition 390 uM [U-100% 13C; U-100% 15N] PRPF40A, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 390 uM [U-100% 13C; U-100% 15N] PRPF40A, 100% D2O \| 100% D2O	Resolution not provided
8PXX Structure of the WW domain tandem of PRPF40A in complex with SF1 Deposited 2023-07-24	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 141–236（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 133；Pressure 1 NMR sample composition 590 uM [U-100% 13C; U-100% 15N] PRPF40A, 590 uM SF1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 590 uM [U-100% 13C; U-100% 15N] PRPF40A, 590 uM SF1, 100% D2O \| 100% D2O NMR sample composition 900 uM [U-100% 13C; U-100% 15N] SF1, 900 uM PRPF40A, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 900 uM [U-100% 13C; U-100% 15N] SF1, 900 uM PRPF40A, 100% D2O \| 100% D2O NMR sample composition 150 uM [U-100% 15N] PRPF40A, 150 uM SF1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 150 uM [U-100% 15N] PRPF40A, 150 uM SF1, 10 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FNBP3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–41； UniProt 142–173

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	1ywi
Deposition date deposition_date	2005-02-18
Structure title title	Structure of the FBP11WW1 domain complexed to the peptide APPTPPPLPP
Keywords keywords	WW domain, Class II, Proline-rich peptides, protein-protein interactions, Structural Protein; STRUCTURAL 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	9.23 Å
Radius of gyration Rg (electron density) rg_electron	9.21 Å
Forward intensity I(0) i0	53213900.00
Molecular weight molecular_weight	60772.0 kDa
Excluded volume excluded_volume	75666 Å³
Envelope volume envelope_volume	7639 Å³
Hydration-shell volume shell_volume	6757 Å³
Envelope diameter envelope_diameter	34.2 Å
Shell Rg shell_rg	15.10 Å
Envelope Rg envelope_rg	10.60 Å
Shape Rg shape_rg	9.10 Å
Total Rg total_rg	9.79 Å
Total atoms total_atoms	8280
Residues n_residues	510
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	32.5 Å
Rg (real space) rg_real	9.25 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	5.3210e+07
I(0) uncertainty (real space) i0_real_error	5.5080e+05
Rg (reciprocal space) rg_reciprocal	9.25 Å
I(0) (reciprocal space) i0_reciprocal	53210000.0000
Solution quality estimate total_estimate	0.8409
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	11.9 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.000
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21240.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.671; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.959

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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) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ywia1
Class class	b — All beta proteins
Fold Fold fold	b.72 — WW domain-like
Superfamily Superfamily superfamily	b.72.1 — WW domain
Family Family family	b.72.1.1 — WW domain

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8. Citations (1)

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Description description	Formin-binding protein 3
Molecular weight formula_weight	4747.1 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	8280

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(DE3)

Description description	Formin
Molecular weight formula_weight	983.2 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/yw/1ywi/1ywi.fit
pddf	/app/data/pr_computation/yw/1ywi/1ywi.pr.out
profile	/app/data/saxs_computation/yw/1ywi/1ywi.dat

Structure of the FBP11WW1 domain complexed to the peptide APPTPPPLPP

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

Formin-binding protein 3

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)