SAXSdb — 2vkc

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1666–1770	Fragment：RESIDUES 1666-1770	No other associated polymer	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

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 2VKC	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 experimental conditions	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
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 method 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
3FAU Crystal Structure of human small-MutS related domain Deposited 2008-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1691–1770（80 aa） Fragment：DNA binding domain Chain B 1691–1770（80 aa） Fragment：DNA binding domain Chain C 1691–1770（80 aa） Fragment：DNA binding domain Chain D 1691–1770（80 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	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
3FAU Crystal Structure of human small-MutS related domain Deposited 2008-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1691–1770（80 aa） Fragment：DNA binding domain Chain D 1691–1770（80 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	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
3FAU Crystal Structure of human small-MutS related domain Deposited 2008-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1691–1770（80 aa） Fragment：DNA binding domain Chain C 1691–1770（80 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	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 other PDB entries and 5 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 31–135； UniProt 1666–1770

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	2vkc
Deposition date deposition_date	2007-12-18
Structure title title	Solution structure of the B3BP Smr domain
Keywords keywords	;HUMAN BCL3 BINDING PROTEIN, ALTERNATIVE SPLICING, HOMOLOGOUS RECOMBINATION, MISMATCH REPAIR, SMALL MUTS RELATED, NUCLEOTIDE-BINDING, ATP-BINDING, UBL CONJUGATION, PHOSPHORYLATION, SMR, B3BP, HYDROLASE, CYTOPLASM, COILED COIL ;; HYDROLASE
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	13.84 Å
Radius of gyration Rg (electron density) rg_electron	13.48 Å
Forward intensity I(0) i0	1379090000.00
Molecular weight molecular_weight	328860.0 kDa
Excluded volume excluded_volume	417750 Å³
Envelope volume envelope_volume	26042 Å³
Hydration-shell volume shell_volume	14216 Å³
Envelope diameter envelope_diameter	53.2 Å
Shell Rg shell_rg	21.34 Å
Envelope Rg envelope_rg	16.10 Å
Shape Rg shape_rg	13.44 Å
Total Rg total_rg	13.74 Å
Total atoms total_atoms	47348
Residues n_residues	2940
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	45.7 Å
Rg (real space) rg_real	13.80 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.3790e+09
I(0) uncertainty (real space) i0_real_error	1.4340e+07
Rg (reciprocal space) rg_reciprocal	13.80 Å
I(0) (reciprocal space) i0_reciprocal	1379000000.0000
Solution quality estimate total_estimate	0.8727
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.4 Å
Skewness Skewness skewness	0.248
Kurtosis Kurtosis kurtosis	-0.093
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	147900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.980

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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	2vkcA00
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	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	NEDD4-BINDING PROTEIN 2
Molecular weight formula_weight	15189.6 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	47348

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

Solution structure of the B3BP Smr 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

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 (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/vk/2vkc/2vkc.fit
pddf	/app/data/pr_computation/vk/2vkc/2vkc.pr.out
profile	/app/data/saxs_computation/vk/2vkc/2vkc.dat