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6kyh

Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas

Method: X-RAY DIFFRACTION Dmax: 172.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SH3 and multiple ankyrin repeat domains protein 3

Mus musculus

UniProt Q4ACU6

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 8–362 Fragment：NTD-ANK tandem Mutation：A42K,L231R,F304Y GTPase HRas × 1 （Q61411） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 8–362 Fragment：NTD-ANK tandem Mutation：A42K,L231R,F304Y GTPase HRas × 1 （Q61411） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 8–362 Fragment：NTD-ANK tandem Mutation：A42K,L231R,F304Y GTPase HRas × 1 （Q61411） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 8–362 Fragment：NTD-ANK tandem Mutation：A42K,L231R,F304Y GTPase HRas × 1 （Q61411） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257

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 6KYH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded BR0 (3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Chain H 637–744（108 aa） Fragment：PDZ domain, residues 637-744
Not recorded BR0 (3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.83 Å R-free 0.283
5IZU A new binding site outside the canonical PDZ domain determines the specific interaction between Shank and SAPAP and their function Deposited 2016-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 533–665（133 aa） Fragment：UNP residues 533-665
Chain C 533–665（133 aa） Fragment：UNP residues 533-665
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；289 K；0.1 M Bis-Tris, 3.0 M NaCl
Resolution 2.49 Å R-free 0.251
6KYK Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 Deposited 2019-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–368（368 aa） Fragment：NTD-ANK tandem
Mutation：L231R,F304Y GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500
Resolution 2.82 Å R-free 0.300
6KYK Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 Deposited 2019-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–368（368 aa） Fragment：NTD-ANK tandem
Mutation：L231R,F304Y GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500
Resolution 2.82 Å R-free 0.300
9KSQ Crystal Structure of the mouse Shank3 SAM domain Deposited 2024-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1654–1730（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20% v/v 2-Propanol
Resolution 2.79 Å R-free 0.255

4 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SHAN3_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–361； UniProt 8–362 Author chain B； PDBConstruct 7–361； UniProt 8–362 Author chain C； PDBConstruct 7–361； UniProt 8–362 Author chain D； PDBConstruct 7–361； UniProt 8–362

GTPase HRas

Mus musculus

UniProt Q61411

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 E； UniProt 1–167 Not recorded SH3 and multiple ankyrin repeat domains protein 3 × 1 （Q4ACU6） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 1–167 Not recorded SH3 and multiple ankyrin repeat domains protein 3 × 1 （Q4ACU6） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 1–167 Not recorded SH3 and multiple ankyrin repeat domains protein 3 × 1 （Q4ACU6） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 1–167 Not recorded SH3 and multiple ankyrin repeat domains protein 3 × 1 （Q4ACU6） GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000 Resolution 3.30 Å R-free 0.257

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name RASH_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 5–171； UniProt 1–167 Author chain F； PDBConstruct 5–171； UniProt 1–167 Author chain G； PDBConstruct 5–171； UniProt 1–167 Author chain H； PDBConstruct 5–171； UniProt 1–167

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 6kyh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6kyh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6kyh
Deposition date deposition_date2019-09-18
Structure title titleCrystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas
Keywords keywordsShank3, GTPase, synaptic scaffold protein, STRUCTURAL PROTEIN-SIGNALING PROTEIN complex; STRUCTURAL PROTEIN/SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier53.00 Å
Radius of gyration Rg (electron density) rg_electron52.80 Å
Forward intensity I(0) i0847555000.00
Molecular weight molecular_weight233690.0 kDa
Excluded volume excluded_volume289180 ų
Envelope volume envelope_volume429410 ų
Hydration-shell volume shell_volume70432 ų
Envelope diameter envelope_diameter176.6 Å
Shell Rg shell_rg53.06 Å
Envelope Rg envelope_rg51.27 Å
Shape Rg shape_rg52.77 Å
Total Rg total_rg52.91 Å
Total atoms total_atoms16429
Residues n_residues2061
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 dmax172.7 Å
Rg (real space) rg_real52.96 Å
Rg uncertainty (real space) rg_real_error1.97 Å
I(0) (real space) i0_real8.4760e+08
I(0) uncertainty (real space) i0_real_error1.7320e+07
Rg (reciprocal space) rg_reciprocal53.01 Å
I(0) (reciprocal space) i0_reciprocal847600000.0000
Solution quality estimate total_estimate0.8853
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.3 Å
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.586
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24050000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.676
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6kyhE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6kyhF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6kyhG00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6kyhH00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)