SAXSdb — 3tmh

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF3

Homo sapiens

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 × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain A； UniProt 375–459 Chain E； UniProt 375–459 Chain I； UniProt 375–459	Fragment：UNP RESIDUES 375-459	cAMP-dependent protein kinase type II-alpha regulatory subunit × 8 （P12368） A-kinase anchor protein 10, mitochondrial × 6 （O43572）	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；100 mM HEPES, pH 7, 20% PEG MME, Microbatch, temperature 293K	Resolution 3.80 Å R-free 0.328

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 3TMH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EEI Solution Structure of Second PDZ domain of PDZ Domain Containing Protein 1 Deposited 2007-02-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 132–224（93 aa） Fragment：pdz domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 3.36mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O \| 10% D20, 90% H2O	Resolution not provided
2EEJ Solution Structure of Fourth PDZ domain of PDZ Domain Containing Protein 1 Deposited 2007-02-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–458（83 aa） Fragment：PDZ domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 2.65mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O \| 90% H2O/10% D2O	Resolution not provided
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 Å R-free 0.267
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 Å R-free 0.267
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 Å R-free 0.267
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 Å R-free 0.267
4Q2P NHERF3 PDZ2 in Complex with a Phage-Derived Peptide Deposited 2014-04-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 132–215（84 aa） Fragment：unp residues 132-215 Chain B 132–215（84 aa） Fragment：unp residues 132-215 Chain C 132–215（84 aa） Fragment：unp residues 132-215	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；292 K；30% PEG 4000, 0.1 M sodium acetate (pH 4.6), 0.1 M magnesium chloride, VAPOR DIFFUSION, temperature 292K	Resolution 2.05 Å R-free 0.252
6EZI PDZK1 domain 4 in complex with C-terminal peptide of human PepT2. Deposited 2017-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 374–460（87 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292.15 K；0.1 M Trisodium citrate pH 6.45 20% PEG 4000 20 %(v/v) isopropanol	Resolution 1.50 Å R-free 0.214
9RXN Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–106（101 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；50 mM Bicine pH 8.4, 12% PEG 600, 3.5% PEG 2000 MME	Resolution 1.36 Å R-free 0.161
9RXN Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 6–106（101 aa）	Not recorded	NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；50 mM Bicine pH 8.4, 12% PEG 600, 3.5% PEG 2000 MME	Resolution 1.36 Å R-free 0.161
9RXO Structure of the PDZ2 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–215（85 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% PEG 1500	Resolution 1.20 Å R-free 0.203
9RXO Structure of the PDZ2 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 131–215（85 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% PEG 1500	Resolution 1.20 Å R-free 0.203
9RXP Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–458（84 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1% 2-methyl-2,4-pentanediol, 2.5 M ammonium sulfate	Resolution 1.43 Å R-free 0.231
9RXP Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 375–458（84 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1% 2-methyl-2,4-pentanediol, 2.5 M ammonium sulfate	Resolution 1.43 Å R-free 0.231
9RXR Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–106（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM MES, pH 6.5, 700 mM NaCl, 18% PEG 4000	Resolution 1.69 Å R-free 0.210
9RXS Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–458（84 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris pH 8.5, 100mM NaCl, 18% PEG 10000, 20% Glycerol	Resolution 2.00 Å R-free 0.242
9RXS Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 375–458（84 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris pH 8.5, 100mM NaCl, 18% PEG 10000, 20% Glycerol	Resolution 2.00 Å R-free 0.242

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NHRF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–87； UniProt 375–459 Author chain E； PDBConstruct 3–87； UniProt 375–459 Author chain I； PDBConstruct 3–87； UniProt 375–459

cAMP-dependent protein kinase type II-alpha regulatory subunit

Rattus norvegicus

UniProt P12368

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 × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain B； UniProt 1–45 Chain C； UniProt 1–45 Chain F； UniProt 1–45 Chain G； UniProt 1–45	Fragment：Dimerization/docking domain (D/D), UNP RESIDUES 3-44	Na(+)/H(+) exchange regulatory cofactor NHE-RF3 × 6 （Q5T2W1） A-kinase anchor protein 10, mitochondrial × 6 （O43572）	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；100 mM HEPES, pH 7, 20% PEG MME, Microbatch, temperature 293K	Resolution 3.80 Å R-free 0.328

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 3TMH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DRN Docking and dimerization domain (D/D) of the Type II-alpha regulatory subunity of protein kinase A (PKA) in complex with a peptide from an A-kinase anchoring protein Deposited 2006-06-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–44（43 aa） Fragment：N-terminal docking and dimerization domain, residues 4-46 Chain B 2–44（43 aa） Fragment：N-terminal docking and dimerization domain, residues 4-46	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Pressure 1 NMR sample composition 2mM RII-alpha(1-44); 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2H9R Docking and dimerization domain (D/D) of the regulatory subunit of the Type II-alpha cAMP-dependent protein kinase A associated with a Peptide derived from an A-kinase anchoring protein (AKAP) Deposited 2006-06-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–44（43 aa） Fragment：N-terminal docking and dimerization domain, residues 4-46 Chain B 2–44（43 aa） Fragment：N-terminal docking and dimerization domain, residues 4-46	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Pressure 1 NMR sample composition 2mM RII-alpha(1-44); 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2HWN Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide Deposited 2006-08-01	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 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain B 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100mM HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.239
2HWN Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide Deposited 2006-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain D 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100mM HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.239
2HWN Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide Deposited 2006-08-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain B 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain C 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain D 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100mM HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.239
2IZY Molecular Basis of AKAP Specificity for PKA Regulatory Subunits Deposited 2006-07-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 2–44（43 aa） Fragment：RESIDUES 2-44 Chain B 2–44（43 aa） Fragment：RESIDUES 2-44 Chain C 2–44（43 aa） Fragment：RESIDUES 2-44 Chain D 2–44（43 aa） Fragment：RESIDUES 2-44 Chain E 2–44（43 aa） Fragment：RESIDUES 2-44 Chain F 2–44（43 aa） Fragment：RESIDUES 2-44 Chain G 2–44（43 aa） Fragment：RESIDUES 2-44 Chain H 2–44（43 aa） Fragment：RESIDUES 2-44	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；8-10% PEG400, 0.2-0.4 M SODIUM PHOSPHATE AND SODIUM CITRATE (PH 5.8)	Resolution 2.20 Å R-free 0.272

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KAP2_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–48； UniProt 1–45 Author chain C； PDBConstruct 4–48； UniProt 1–45 Author chain F； PDBConstruct 4–48； UniProt 1–45 Author chain G； PDBConstruct 4–48； UniProt 1–45

A-kinase anchor protein 10, mitochondrial

Homo sapiens

UniProt O43572

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 × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain D； UniProt 623–662 Chain H； UniProt 623–662 Chain L； UniProt 623–662	Fragment：A-kinase binding domain (AKB), UNP RESIDUES 623-662	Na(+)/H(+) exchange regulatory cofactor NHE-RF3 × 6 （Q5T2W1） cAMP-dependent protein kinase type II-alpha regulatory subunit × 8 （P12368）	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；100 mM HEPES, pH 7, 20% PEG MME, Microbatch, temperature 293K	Resolution 3.80 Å R-free 0.328

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 3TMH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3IM4 Crystal structure of cAMP-dependent Protein Kinase A Regulatory Subunit I alpha in complex with dual-specific A-Kinase Anchoring Protein 2 Deposited 2009-08-09	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 C 623–662（40 aa） Fragment：PKA-RII subunit binding: UNP residues 623-662	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.5；298 K；10% PEG 6000, 0.01 M ZnCl2, 0.1 M MES, pH 5.5, MICROBATCH, temperature 298K	Resolution 2.29 Å R-free 0.254

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AKA10_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 6–45； UniProt 623–662 Author chain H； PDBConstruct 6–45； UniProt 623–662 Author chain L； PDBConstruct 6–45； UniProt 623–662

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	3tmh
Deposition date deposition_date	2011-08-31
Structure title title	Crystal structure of dual-specific A-kinase anchoring protein 2 in complex with cAMP-dependent protein kinase A type II alpha and PDZK1
Keywords keywords	alpha helical bundle, PDZ fold, Anchoring protein, PKA, PDZ proteins, membrane, TRANSPORT PROTEIN-SIGNALING PROTEIN complex; TRANSPORT PROTEIN/SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	31.22 Å
Radius of gyration Rg (electron density) rg_electron	30.51 Å
Forward intensity I(0) i0	40201100.00
Molecular weight molecular_weight	50309.0 kDa
Excluded volume excluded_volume	63405 Å³
Envelope volume envelope_volume	89515 Å³
Hydration-shell volume shell_volume	26180 Å³
Envelope diameter envelope_diameter	101.6 Å
Shell Rg shell_rg	35.51 Å
Envelope Rg envelope_rg	29.13 Å
Shape Rg shape_rg	30.53 Å
Total Rg total_rg	30.95 Å
Total atoms total_atoms	3545
Residues n_residues	471
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	94.6 Å
Rg (real space) rg_real	31.17 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	4.0200e+07
I(0) uncertainty (real space) i0_real_error	6.0820e+05
Rg (reciprocal space) rg_reciprocal	31.19 Å
I(0) (reciprocal space) i0_reciprocal	40200000.0000
Solution quality estimate total_estimate	0.9052
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.6 Å
Skewness Skewness skewness	0.145
Kurtosis Kurtosis kurtosis	-0.610
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3536000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.868

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Molecular weight formula_weight	9277.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I
Atom count atom_count	3553

GSKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCGKKA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	cAMP-dependent protein kinase type II-alpha regulatory subunit
Molecular weight formula_weight	5542.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,F,G

GSHMGHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR

来源 Source

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

Entity 3 Entity 3 polymer

Description description	A-kinase anchor protein 10, mitochondrial
Molecular weight formula_weight	5086.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L

GSPEFVQGNTDEAQEELAWKIAKMIVSDVMQQAQYDQPLEKSTKL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3tmhA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3tmhE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3tmhI00
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	121.472 Å
Unit-cell length b length_b	121.472 Å
Unit-cell length c length_c	88.282 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	50.038 Å
R factor r_factor	0.2727
R_work r_work	0.2683
R_free r_free	0.3284

fit	/app/data/saxs_computation/tm/3tmh/3tmh.fit
pddf	/app/data/pr_computation/tm/3tmh/3tmh.pr.out
profile	/app/data/saxs_computation/tm/3tmh/3tmh.dat

Crystal structure of dual-specific A-kinase anchoring protein 2 in complex with cAMP-dependent protein kinase A type II alpha and PDZK1

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF3

State in the Current Structure

Other States of the Same Protein in the Database

cAMP-dependent protein kinase type II-alpha regulatory subunit

State in the Current Structure

Other States of the Same Protein in the Database

A-kinase anchor protein 10, mitochondrial

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)