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2d9i

Solution structure of the SMR domain of NEDD4-binding protein 2

Method: SOLUTION NMR Dmax: 55.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NEDD4-binding protein 2

Homo sapiens

UniProt Q86UW6

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 1688–1770 Fragment：SMR domain No other associated polymer 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

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 2D9I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2VKC Solution structure of the B3BP Smr domain Deposited 2007-12-18 Different construct Different experimental conditions 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 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 8–90； UniProt 1688–1770

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2d9i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2d9i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2d9i
Deposition date deposition_date2005-12-09
Structure title titleSolution structure of the SMR domain of NEDD4-binding protein 2
Keywords keywords;SMR domain, Nedd4-binding protein 2, N4BP2, BCL-3 binding protein, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, APOPTOSIS ;; APOPTOSIS
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.92 Å
Radius of gyration Rg (electron density) rg_electron13.95 Å
Forward intensity I(0) i0604621000.00
Molecular weight molecular_weight206340.0 kDa
Excluded volume excluded_volume258460 ų
Envelope volume envelope_volume37063 ų
Hydration-shell volume shell_volume17287 ų
Envelope diameter envelope_diameter61.8 Å
Shell Rg shell_rg24.24 Å
Envelope Rg envelope_rg18.77 Å
Shape Rg shape_rg13.96 Å
Total Rg total_rg14.19 Å
Total atoms total_atoms29340
Residues n_residues1920
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax55.4 Å
Rg (real space) rg_real14.94 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real6.0460e+08
I(0) uncertainty (real space) i0_real_error8.1160e+06
Rg (reciprocal space) rg_reciprocal14.94 Å
I(0) (reciprocal space) i0_reciprocal604600000.0000
Solution quality estimate total_estimate0.7211
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.8 Å
Skewness Skewness skewness0.402
Kurtosis Kurtosis kurtosis0.019
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha290500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.499; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.879; Smooth: 0.000
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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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2d9ia1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.8 — SMR domain-like
Family Family familyd.68.8.1 — Smr domain
Domain ID domain_idd2d9ia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2d9ia3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2d9iA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily110 —
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8. Citations (1)

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9. Files and Curves (10)