4hop

Crystal structure of the computationally designed NNOS-Syntrophin complex

Method: X-RAY DIFFRACTION Dmax: 112.3 Å Quality: GOOD

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

Alpha-1-syntrophin

Mus musculus

UniProt Q61234

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 77–162 Fragment:PDZ DOMAIN (RESIDUES 77-162) Mutation:H142F Nitric oxide synthase, brain × 1 (P29476) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.25;293 K;0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.29 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 77–162 Fragment:PDZ DOMAIN (RESIDUES 77-162) Mutation:H142F Nitric oxide synthase, brain × 1 (P29476) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.25;293 K;0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.29 Å R-free 0.273
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 77–162 Fragment:PDZ DOMAIN (RESIDUES 77-162) Mutation:H142F Nitric oxide synthase, brain × 1 (P29476) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.25;293 K;0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.29 Å R-free 0.273

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.

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

View Construct and Data Evidence
UniProt name SNTA1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–88; UniProt 77–162 Author chain C; PDBConstruct 3–88; UniProt 77–162 Author chain E; PDBConstruct 3–88; UniProt 77–162

Nitric oxide synthase, brain

Rattus norvegicus

UniProt P29476

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 4–126 Fragment:PDZ DOMAIN (RESIDUES 4-126) Mutation:T109M Alpha-1-syntrophin × 1 (Q61234) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.25;293 K;0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.29 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 4–126 Fragment:PDZ DOMAIN (RESIDUES 4-126) Mutation:T109M Alpha-1-syntrophin × 1 (Q61234) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.25;293 K;0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.29 Å R-free 0.273
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 4–126 Fragment:PDZ DOMAIN (RESIDUES 4-126) Mutation:T109M Alpha-1-syntrophin × 1 (Q61234) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.25;293 K;0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.29 Å R-free 0.273

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.

348 other PDB entries and 349 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOS1_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–123; UniProt 4–126 Author chain D; PDBConstruct 1–123; UniProt 4–126 Author chain F; PDBConstruct 1–123; UniProt 4–126

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 4hop

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4hop
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4hop
Deposition date deposition_date2012-10-22
Structure title titleCrystal structure of the computationally designed NNOS-Syntrophin complex
Keywords keywordsPDZ, Protein Binding, Dimerization, Mutation, Membrane, MEMBRANE PROTEIN-OXIDOREDUCTASE complex; MEMBRANE PROTEIN/OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.82
Radius of gyration Rg (electron density) rg_electron33.59
Forward intensity I(0) i066548500.00
Molecular weight molecular_weight66772.0 kDa
Excluded volume excluded_volume84904 ų
Envelope volume envelope_volume116490 ų
Hydration-shell volume shell_volume31184 ų
Envelope diameter envelope_diameter120.6
Shell Rg shell_rg37.43
Envelope Rg envelope_rg33.03
Shape Rg shape_rg33.58
Total Rg total_rg33.94
Total atoms total_atoms4702
Residues n_residues625
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax112.3
Rg (real space) rg_real33.98
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real6.6550e+07
I(0) uncertainty (real space) i0_real_error1.0050e+06
Rg (reciprocal space) rg_reciprocal33.88
I(0) (reciprocal space) i0_reciprocal66540000.0000
Solution quality estimate total_estimate0.8693
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.6
Skewness Skewness skewness0.418
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7863000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.834; Smooth: 0.863

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4hopA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
Domain ID domain_id4hopB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
Domain ID domain_id4hopC00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
Domain ID domain_id4hopD00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
Domain ID domain_id4hopE00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
Domain ID domain_id4hopF00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain

8. Citations (1)

9. Files and Curves (10)