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2g5m

Spinophilin PDZ domain

Method: SOLUTION NMR Dmax: 47.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurabin-2

Rattus norvegicus

UniProt O35274

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 B； UniProt 493–602 Fragment：PDZ domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 20 mM Na phosphate; 50 mM NaCl；Pressure ambient NMR sample composition：1.8 mM PDZ domain, 15N samples; 20 mM Na phosphate buffer 50 mM NaCl, pH 6.5; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：1.8 mM PDZ domain, 13C/15N samples; 20 mM Na phosphate buffer 50 mM NaCl, pH 6.5; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：1.8 mM PDZ domain, 13C/15N samples; 20 mM Na phosphate buffer 50 mM NaCl, pH 6.5; 90% H2O, 10% D2O | 100% d20 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 2G5M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3EGG Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Spinophilin Deposited 2008-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 417–583（167 aa） Fragment：PP1 binding and PDZ domains
Not recorded GOL GLYCEROL × 4 MN MANGANESE (II) ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2M NaCl, 0.1M MES, 10% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.85 Å R-free 0.211
3EGG Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Spinophilin Deposited 2008-09-10 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 D 417–583（167 aa） Fragment：PP1 binding and PDZ domains
Not recorded GOL GLYCEROL × 3 MN MANGANESE (II) ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2M NaCl, 0.1M MES, 10% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.85 Å R-free 0.211
3EGH Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R Deposited 2008-09-10 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 × 6 PDB declaration: hexameric
Chain C 417–583（167 aa） Fragment：PP1 binding and PDZ domains
Chain D 417–583（167 aa） Fragment：PP1 binding and PDZ domains
Not recorded GOL GLYCEROL × 4 MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；277 K；0.1M MES, 15% PEG 550 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.235
3EGH Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R Deposited 2008-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 417–583（167 aa） Fragment：PP1 binding and PDZ domains
Not recorded GOL GLYCEROL × 4 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；277 K；0.1M MES, 15% PEG 550 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.235
3EGH Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R Deposited 2008-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 417–583（167 aa） Fragment：PP1 binding and PDZ domains
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；277 K；0.1M MES, 15% PEG 550 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.235

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEB2_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 4–113； UniProt 493–602

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 2g5m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2g5m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2g5m
Deposition date deposition_date2006-02-23
Structure title titleSpinophilin PDZ domain
Keywords keywordsSpinophilin, PDZ domain, CNS, synaptic transmission, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.27 Å
Radius of gyration Rg (electron density) rg_electron16.63 Å
Forward intensity I(0) i0879207000.00
Molecular weight molecular_weight242340.0 kDa
Excluded volume excluded_volume301090 ų
Envelope volume envelope_volume75236 ų
Hydration-shell volume shell_volume25691 ų
Envelope diameter envelope_diameter84.8 Å
Shell Rg shell_rg31.89 Å
Envelope Rg envelope_rg25.95 Å
Shape Rg shape_rg16.62 Å
Total Rg total_rg17.13 Å
Total atoms total_atoms34120
Residues n_residues2260
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 dmax47.9 Å
Rg (real space) rg_real16.26 Å
Rg uncertainty (real space) rg_real_error0.09 Å
I(0) (real space) i0_real8.4010e+08
I(0) uncertainty (real space) i0_real_error7.8450e+06
Rg (reciprocal space) rg_reciprocal17.46 Å
I(0) (reciprocal space) i0_reciprocal879200000.0000
Solution quality estimate total_estimate0.6586
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary18.3 Å
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.231
Angular range angular_range— – 0.4600 Å−1
Current regularization parameter α current_alpha3.6040
Highest regularization parameter α highest_alpha376300.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.879; Stabil: 0.976; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; 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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2g5mb1
Class classb — All beta proteins
Fold Fold foldb.36 — PDZ domain-like
Superfamily Superfamily superfamilyb.36.1 — PDZ domain-like
Family Family familyb.36.1.0 — automated matches
Domain ID domain_idd2g5mb2
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_id2g5mB01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
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8. Citations (1)

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9. Files and Curves (10)