SAXSdb — 9f6s

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

PDZ and LIM domain protein 5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–85	Not recorded	AP2-associated protein kinase 1 × 1 （Q2M2I8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 2.0 M Ammonium sulfate, 0.1 M Sodium cacodylate 6.5	Resolution 1.00 Å R-free 0.213

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 9F6S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DAR Solution structure of first LIM domain of Enigma-like PDZ and LIM domains protein Deposited 2005-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 399–475（77 aa） Fragment：LIM domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1.39mM LIM domain; U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2 ; 1mM IDA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	PDLI5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–90； UniProt 1–85

AP2-associated protein kinase 1

Homo sapiens

UniProt Q2M2I8

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 956–961	Not recorded	PDZ and LIM domain protein 5 × 1 （Q96HC4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 2.0 M Ammonium sulfate, 0.1 M Sodium cacodylate 6.5	Resolution 1.00 Å R-free 0.213

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 9F6S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WSQ Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with small molecule inhibitor Deposited 2014-10-28	Different construct 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 29–345（317 aa） Fragment：kinase domain, UNP residues 29-345	Not recorded	ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 1 KSA K-252A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.005M zinc acetate, 20% PEG3350	Resolution 1.95 Å R-free 0.208
4WSQ Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with small molecule inhibitor Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–345（317 aa） Fragment：kinase domain, UNP residues 29-345	Not recorded	ZN ZINC ION × 3 KSA K-252A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.005M zinc acetate, 20% PEG3350	Resolution 1.95 Å R-free 0.208
5L4Q Crystal Structure of Adaptor Protein 2 Associated Kinase 1 (AAK1) in Complex with LKB1 (AAK1 Dual Inhibitor) Deposited 2016-05-26	Different construct 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 27–365（339 aa）	Not recorded	LKB ~{N}-[5-(4-cyanophenyl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M bis-tris pH 5.5, 26% PEG3350	Resolution 1.97 Å R-free 0.227
5L4Q Crystal Structure of Adaptor Protein 2 Associated Kinase 1 (AAK1) in Complex with LKB1 (AAK1 Dual Inhibitor) Deposited 2016-05-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–365（339 aa）	Not recorded	LKB ~{N}-[5-(4-cyanophenyl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M bis-tris pH 5.5, 26% PEG3350	Resolution 1.97 Å R-free 0.227
5TE0 Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with BIBF 1120 Deposited 2016-09-20	Different construct 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 27–365（339 aa） Fragment：UNP residues 27-365	Not recorded	XIN methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25 % PEG 3350, 0.1M BIS-TRIS, 0.2M Lithium Sulfate	Resolution 1.90 Å R-free 0.199
8GMC CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH 5-[(4-aminopiperidin-1-yl)methyl]-N-{3-[5-(propan-2-yl)-1,3,4-thiadiazol-2-yl]phenyl}pyrrolo[2,1-f][1,2,4]triazin-4-amine Deposited 2023-03-24	Different construct 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 26–330（305 aa）	Not recorded	YFV 5-[(4-aminopiperidin-1-yl)methyl]-N-{3-[5-(propan-2-yl)-1,3,4-thiadiazol-2-yl]phenyl}pyrrolo[2,1-f][1,2,4]triazin-4-amine × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；1.2M AmSO4, 0.1M tri-Na Citrate pH 6.0, 3% isopropanol, 296K	Resolution 2.50 Å R-free 0.256
8GMC CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH 5-[(4-aminopiperidin-1-yl)methyl]-N-{3-[5-(propan-2-yl)-1,3,4-thiadiazol-2-yl]phenyl}pyrrolo[2,1-f][1,2,4]triazin-4-amine Deposited 2023-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–330（305 aa）	Not recorded	YFV 5-[(4-aminopiperidin-1-yl)methyl]-N-{3-[5-(propan-2-yl)-1,3,4-thiadiazol-2-yl]phenyl}pyrrolo[2,1-f][1,2,4]triazin-4-amine × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；1.2M AmSO4, 0.1M tri-Na Citrate pH 6.0, 3% isopropanol, 296K	Resolution 2.50 Å R-free 0.256
8GMD CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH (5P)-3-({(8R)-5-[(4-aminopiperidin-1-yl)methyl]pyrrolo[2,1-f][1,2,4]triazin-4-yl}amino)-5-[2-(propan-2-yl)-2H-tetrazol-5-yl]phenol Deposited 2023-03-24	Different construct 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 26–330（305 aa）	Not recorded	ZRR (5P)-3-({(8R)-5-[(4-aminopiperidin-1-yl)methyl]pyrrolo[2,1-f][1,2,4]triazin-4-yl}amino)-5-[2-(propan-2-yl)-2H-tetrazol-5-yl]phenol × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；1.2M AmSO4, 0.1M tri-Na Citrate pH 6.0, 3% isopropanol, 296K	Resolution 2.20 Å R-free 0.250
8GMD CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH (5P)-3-({(8R)-5-[(4-aminopiperidin-1-yl)methyl]pyrrolo[2,1-f][1,2,4]triazin-4-yl}amino)-5-[2-(propan-2-yl)-2H-tetrazol-5-yl]phenol Deposited 2023-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–330（305 aa）	Not recorded	ZRR (5P)-3-({(8R)-5-[(4-aminopiperidin-1-yl)methyl]pyrrolo[2,1-f][1,2,4]triazin-4-yl}amino)-5-[2-(propan-2-yl)-2H-tetrazol-5-yl]phenol × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；1.2M AmSO4, 0.1M tri-Na Citrate pH 6.0, 3% isopropanol, 296K	Resolution 2.20 Å R-free 0.250
9F8T Clathrin terminal domain complexed with C-terminus of AAK1L Deposited 2024-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 956–961（6 aa） Chain E 956–961（6 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；20% PEG 3,350; 100 mM Bis-Tris propane, pH 6.0; 200 mM sodium citrate; 10 mM DTT	Resolution 1.71 Å R-free 0.209
9QB5 AP2-associated protein kinase 1 (AAK1) bound to CKJB68 Deposited 2025-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–345（317 aa） Chain B 29–345（317 aa）	Not recorded	F7I ~{N}-(phenylmethyl)-7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxamide × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；0.2 M ammonium sulfate 30% PEG4000	Resolution 2.00 Å R-free 0.227

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AAK1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–6； UniProt 956–961

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	9f6s
Deposition date deposition_date	2024-05-02
Structure title title	PDZ domain in complex with the peptide from AP2-associated protein kinase 1
Keywords keywords	PDZ; AP2; kinase;, CYTOSOLIC PROTEIN; CYTOSOLIC 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	13.31 Å
Radius of gyration Rg (electron density) rg_electron	11.75 Å
Forward intensity I(0) i0	2008860.00
Molecular weight molecular_weight	9398.0 kDa
Excluded volume excluded_volume	11700 Å³
Envelope volume envelope_volume	13062 Å³
Hydration-shell volume shell_volume	9569 Å³
Envelope diameter envelope_diameter	37.9 Å
Shell Rg shell_rg	17.36 Å
Envelope Rg envelope_rg	12.02 Å
Shape Rg shape_rg	11.75 Å
Total Rg total_rg	13.14 Å
Total atoms total_atoms	1318
Residues n_residues	90
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	40.9 Å
Rg (real space) rg_real	13.19 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	2.0090e+06
I(0) uncertainty (real space) i0_real_error	2.3020e+04
Rg (reciprocal space) rg_reciprocal	13.20 Å
I(0) (reciprocal space) i0_reciprocal	2009000.0000
Solution quality estimate total_estimate	0.8925
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.1 Å
Skewness Skewness skewness	0.031
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	386800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PDZ and LIM domain protein 5
Molecular weight formula_weight	9355.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1518

GPLGSMSNYSVSLVGPAPWGFRLQGGKDFNMPLTISSLKDGGKAAQANVRIGDVVLSIDGINAQGMTHLEAQNKIKGCTGSLNMTLQRAS

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	AP2-associated protein kinase 1
Molecular weight formula_weight	715.8 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DQLIDL

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 BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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8. Citations (1)

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Unit-cell length a length_a	36.930 Å
Unit-cell length b length_b	37.840 Å
Unit-cell length c length_c	52.390 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.000 Å
Low-resolution limit resolution_low	30.680 Å
R factor r_factor	0.2004
R_work r_work	0.2000
R_free r_free	0.2134

fit	/app/data/saxs_computation/f6/9f6s/9f6s.fit
pddf	/app/data/pr_computation/f6/9f6s/9f6s.pr.out
profile	/app/data/saxs_computation/f6/9f6s/9f6s.dat

PDZ domain in complex with the peptide from AP2-associated protein kinase 1

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

PDZ and LIM domain protein 5

State in the Current Structure

Other States of the Same Protein in the Database

AP2-associated protein kinase 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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)