SAXSdb — 3fau

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

NEDD4-binding protein 2

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1691–1770 Chain B； UniProt 1691–1770 Chain C； UniProt 1691–1770 Chain D； UniProt 1691–1770	Fragment：DNA binding domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 7；293 K；0.1M Ammonium Chloride, 0.1M Mops (pH 7.0), 40% PEG 2000mme, hanging drop, temperature 293K	Resolution 1.90 Å R-free 0.242
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1691–1770 Chain D； UniProt 1691–1770	Fragment：DNA binding domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 7；293 K；0.1M Ammonium Chloride, 0.1M Mops (pH 7.0), 40% PEG 2000mme, hanging drop, temperature 293K	Resolution 1.90 Å R-free 0.242
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1691–1770 Chain C； UniProt 1691–1770	Fragment：DNA binding domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 7；293 K；0.1M Ammonium Chloride, 0.1M Mops (pH 7.0), 40% PEG 2000mme, hanging drop, temperature 293K	Resolution 1.90 Å R-free 0.242

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 3FAU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2D9I Solution structure of the SMR domain of NEDD4-binding protein 2 Deposited 2005-12-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1688–1770（83 aa） Fragment：SMR domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.99mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0);100mM NaCl; 1mM d-DTT; 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2VKC Solution structure of the B3BP Smr domain Deposited 2007-12-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1666–1770（105 aa） Fragment：RESIDUES 1666-1770	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；308 K；Ionic strength (raw mmCIF value) 200；Pressure 1.0 NMR sample composition 95% WATER/5% D2O	Resolution not provided
3BHB Crystal Structure of KMD Phosphopeptide Bound to Human Class I MHC HLA-A2 Deposited 2007-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 129–138（10 aa） Fragment：UNP residues 129-138	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% POLYACRYLIC ACID, 0.1M HEPES, 0.09M MgCl2, pH 7.5, VAPOR DIFFUSION, hanging drop, temperature 298K	Resolution 2.20 Å R-free 0.256

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	N4BP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–82； UniProt 1691–1770 Author chain B； PDBConstruct 3–82； UniProt 1691–1770 Author chain C； PDBConstruct 3–82； UniProt 1691–1770 Author chain D； PDBConstruct 3–82； UniProt 1691–1770

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	3fau
Deposition date deposition_date	2008-11-18
Structure title title	Crystal Structure of human small-MutS related domain
Keywords keywords	;smr, small-MutS related domain, nicking endonuclease, Alternative splicing, ATP-binding, Coiled coil, Cytoplasm, Hydrolase, Nucleotide-binding, Phosphoprotein, Polymorphism, Ubl conjugation ;; HYDROLASE
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	22.42 Å
Radius of gyration Rg (electron density) rg_electron	21.14 Å
Forward intensity I(0) i0	19341300.00
Molecular weight molecular_weight	34590.0 kDa
Excluded volume excluded_volume	44075 Å³
Envelope volume envelope_volume	55218 Å³
Hydration-shell volume shell_volume	22224 Å³
Envelope diameter envelope_diameter	81.3 Å
Shell Rg shell_rg	27.45 Å
Envelope Rg envelope_rg	21.32 Å
Shape Rg shape_rg	21.14 Å
Total Rg total_rg	22.04 Å
Total atoms total_atoms	2432
Residues n_residues	308
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	80.7 Å
Rg (real space) rg_real	22.36 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	1.9340e+07
I(0) uncertainty (real space) i0_real_error	2.7560e+05
Rg (reciprocal space) rg_reciprocal	22.38 Å
I(0) (reciprocal space) i0_reciprocal	19340000.0000
Solution quality estimate total_estimate	0.8469
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.307
Kurtosis Kurtosis kurtosis	-0.155
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4753000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.678; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.992

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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) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3faua1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.8 — SMR domain-like
Family Family family	d.68.8.1 — Smr domain

Domain ID domain_id	d3faua2
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	d3faub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.8 — SMR domain-like
Family Family family	d.68.8.1 — Smr domain

Domain ID domain_id	d3faub2
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	d3fauc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.8 — SMR domain-like
Family Family family	d.68.8.1 — Smr domain

Domain ID domain_id	d3fauc2
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	d3faud1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.8 — SMR domain-like
Family Family family	d.68.8.1 — Smr domain

Domain ID domain_id	d3faud2
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

CATH v4.4 (4 domains)

Domain ID domain_id	3fauA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3fauB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3fauC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3fauD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	110 —

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8. Citations (1)

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Unit-cell length a length_a	34.490 Å
Unit-cell length b length_b	57.106 Å
Unit-cell length c length_c	71.356 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	44.419 Å
R factor r_factor	0.1900
R_work r_work	0.1870
R_free r_free	0.2420

Description description	NEDD4-binding protein 2
Molecular weight formula_weight	9157.7 kDa
EC 编号 ec_number	3.-.-.-
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2736

Crystal Structure of human small-MutS related domain

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

NEDD4-binding protein 2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	304

fit	/app/data/saxs_computation/fa/3fau/3fau.fit
pddf	/app/data/pr_computation/fa/3fau/3fau.pr.out
profile	/app/data/saxs_computation/fa/3fau/3fau.dat