← Back to search
2gle

Solution structure of neurabin SAM domain

Method: SOLUTION NMR Dmax: 34.3 Å Quality: GOOD
▼

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

Neurabin-1

Rattus norvegicus

UniProt O35867

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 986–1056 Fragment：SAM domain (residues 986-1056) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient NMR sample composition：2mM Neurabin SAM U-15N,13C, 20mM phosphate buffer Na, pH 6.8, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：2mM Neurabin SAM U-15N, 20mM phosphate buffer Na, pH 6.8, 90% H2O, 10% | 90% H2O/10% D2O NMR sample composition：2mM Neurabin SAM, 0mM phosphate buffer Na, pH 6.8, 100 % D2O | 100% 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 2GLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2FN5 NMR Structure of the Neurabin PDZ domain (502-594) Deposited 2006-01-10 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 502–594（93 aa） Fragment：PDZ domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient
NMR sample composition 3.5 mM Neurabin PDZ 502-594 U-15N,13C, 20 mM Naphosphate buffer pH 6.5, 50 mM NaCl, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 3.5 mM Neurabin PDZ 502-594 U-15N, 20 mM Naphosphate buffer pH 6.5, 50 mM NaCl, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3HVQ Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Neurabin Deposited 2009-06-16 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 × 4 PDB declaration: tetrameric
Chain C 426–592（167 aa） Fragment：PP1 BINDING AND PDZ DOMAINS
Chain D 426–592（167 aa） Fragment：PP1 BINDING AND PDZ DOMAINS
Not recorded MN MANGANESE (II) ION × 4 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.221
3HVQ Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Neurabin Deposited 2009-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 426–592（167 aa） Fragment：PP1 BINDING AND PDZ DOMAINS
Not recorded MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.221
3HVQ Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Neurabin Deposited 2009-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 426–592（167 aa） Fragment：PP1 BINDING AND PDZ DOMAINS
Not recorded MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.221

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEB1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–74； UniProt 986–1056

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 2gle

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gle
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2gle
Deposition date deposition_date2006-04-04
Structure title titleSolution structure of neurabin SAM domain
Keywords keywordsSAM domain, Scaffold, Protein protein interaction, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.51 Å
Radius of gyration Rg (electron density) rg_electron11.08 Å
Forward intensity I(0) i0388104000.00
Molecular weight molecular_weight166850.0 kDa
Excluded volume excluded_volume209180 ų
Envelope volume envelope_volume14097 ų
Hydration-shell volume shell_volume10034 ų
Envelope diameter envelope_diameter38.3 Å
Shell Rg shell_rg17.71 Å
Envelope Rg envelope_rg12.29 Å
Shape Rg shape_rg11.02 Å
Total Rg total_rg11.40 Å
Total atoms total_atoms23620
Residues n_residues1480
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax34.3 Å
Rg (real space) rg_real11.41 Å
Rg uncertainty (real space) rg_real_error0.20 Å
I(0) (real space) i0_real3.8810e+08
I(0) uncertainty (real space) i0_real_error3.7510e+06
Rg (reciprocal space) rg_reciprocal11.41 Å
I(0) (reciprocal space) i0_reciprocal388100000.0000
Solution quality estimate total_estimate0.8899
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.6 Å
Skewness Skewness skewness-0.045
Kurtosis Kurtosis kurtosis-0.343
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha100900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.994
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2gleA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
▶

8. Citations (1)

▶

9. Files and Curves (10)