SAXSdb — 2l5f

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

Pre-mRNA-processing factor 40 homolog A

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 133–220	Fragment：WW domains (UNP RESIDUES 133-220) Mutation：P67T	No other associated polymer	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

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 2L5F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YWI Structure of the FBP11WW1 domain complexed to the peptide APPTPPPLPP Deposited 2005-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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, 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
1YWJ Structure of the FBP11WW1 domain Deposited 2005-02-18	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification 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
2L9V NMR structure of the FF domain L24A mutant's folding transition state Deposited 2011-02-24	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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	PR40A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–90； UniProt 133–220

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	2l5f
Deposition date deposition_date	2010-11-01
Structure title title	Solution structure of the tandem WW domains from HYPA/FBP11
Keywords keywords	2WW, HYPA, FBP11, PROTEIN BINDING; PROTEIN BINDING
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	13.56 Å
Radius of gyration Rg (electron density) rg_electron	13.53 Å
Forward intensity I(0) i0	170610000.00
Molecular weight molecular_weight	105330.0 kDa
Excluded volume excluded_volume	129940 Å³
Envelope volume envelope_volume	25864 Å³
Hydration-shell volume shell_volume	14074 Å³
Envelope diameter envelope_diameter	54.0 Å
Shell Rg shell_rg	21.46 Å
Envelope Rg envelope_rg	16.19 Å
Shape Rg shape_rg	13.48 Å
Total Rg total_rg	13.96 Å
Total atoms total_atoms	14430
Residues n_residues	920
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	51.0 Å
Rg (real space) rg_real	13.59 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.7060e+08
I(0) uncertainty (real space) i0_real_error	1.9790e+06
Rg (reciprocal space) rg_reciprocal	13.59 Å
I(0) (reciprocal space) i0_reciprocal	170600000.0000
Solution quality estimate total_estimate	0.8130
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	0.007
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	301900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.597; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.779; Smooth: 0.996

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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) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2l5fa1
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.72.1.0 — automated matches

Domain ID domain_id	d2l5fa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2l5fa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (1)

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Description description	Pre-mRNA-processing factor 40 homolog A
Molecular weight formula_weight	10549.5 kDa
Mutation mutation	P67T
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	14430

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

fit	/app/data/saxs_computation/l5/2l5f/2l5f.fit
pddf	/app/data/pr_computation/l5/2l5f/2l5f.pr.out
profile	/app/data/saxs_computation/l5/2l5f/2l5f.dat

Solution structure of the tandem WW domains from HYPA/FBP11

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

Pre-mRNA-processing factor 40 homolog A

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) 3 domains

SCOP 2.08 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)