SAXSdb — 2fn5

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

Neurabin-1

Rattus norvegicus

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 502–594	Fragment：PDZ domain	No other associated polymer	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

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 2FN5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GLE Solution structure of neurabin SAM domain Deposited 2006-04-04	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 986–1056（71 aa） Fragment：SAM domain (residues 986-1056)	Not recorded	No recorded non-water small molecule	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
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 4–94； UniProt 502–594

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	2fn5
Deposition date deposition_date	2006-01-10
Structure title title	NMR Structure of the Neurabin PDZ domain (502-594)
Keywords keywords	PDZ, Neurabin, SIGNALING PROTEIN; SIGNALING PROTEIN
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	13.30 Å
Radius of gyration Rg (electron density) rg_electron	12.54 Å
Forward intensity I(0) i0	556318000.00
Molecular weight molecular_weight	198330.0 kDa
Excluded volume excluded_volume	248040 Å³
Envelope volume envelope_volume	20451 Å³
Hydration-shell volume shell_volume	12337 Å³
Envelope diameter envelope_diameter	50.2 Å
Shell Rg shell_rg	19.84 Å
Envelope Rg envelope_rg	14.64 Å
Shape Rg shape_rg	12.54 Å
Total Rg total_rg	12.65 Å
Total atoms total_atoms	28100
Residues n_residues	1880
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	45.4 Å
Rg (real space) rg_real	13.25 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	5.5630e+08
I(0) uncertainty (real space) i0_real_error	6.5660e+06
Rg (reciprocal space) rg_reciprocal	13.26 Å
I(0) (reciprocal space) i0_reciprocal	556300000.0000
Solution quality estimate total_estimate	0.8409
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.6 Å
Skewness Skewness skewness	0.265
Kurtosis Kurtosis kurtosis	-0.017
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	204800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.644; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

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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_id	d2fn5a1
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d2fn5a2
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 (1 domains)

Domain ID domain_id	2fn5A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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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	Neurabin-1
Molecular weight formula_weight	9948.3 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	28100

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

NMR Structure of the Neurabin PDZ domain (502-594)

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

Neurabin-1

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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/fn/2fn5/2fn5.fit
pddf	/app/data/pr_computation/fn/2fn5/2fn5.pr.out
profile	/app/data/saxs_computation/fn/2fn5/2fn5.dat