SAXSdb — 3dak

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

Serine/threonine-protein kinase OSR1

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 6–295 Chain B； UniProt 6–295 Chain C； UniProt 6–295 Chain D； UniProt 6–295	Fragment：Protein kinase domain, UNP residues 6-295	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Tri-Lithium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.267
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 6–295 Chain D； UniProt 6–295	Fragment：Protein kinase domain, UNP residues 6-295	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Tri-Lithium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.267
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 6–295 Chain C； UniProt 6–295	Fragment：Protein kinase domain, UNP residues 6-295	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Tri-Lithium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.267

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 3DAK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V3S Structural insights into the recognition of substrates and activators by the OSR1 kinase Deposited 2007-06-21	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 433–527（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.239
2V3S Structural insights into the recognition of substrates and activators by the OSR1 kinase Deposited 2007-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 433–527（95 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.239
2VWI Structure of the OSR1 kinase, a hypertension drug target Deposited 2008-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–303（303 aa） Fragment：KINASE DOMAIN, RESIDUES 1-303 Chain B 1–303（303 aa） Fragment：KINASE DOMAIN, RESIDUES 1-303 Chain C 1–303（303 aa） Fragment：KINASE DOMAIN, RESIDUES 1-303 Chain D 1–303（303 aa） Fragment：KINASE DOMAIN, RESIDUES 1-303	Not recorded	AU GOLD ION × 11 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.287
7OKW 1.62A X-ray crystal structure of the conserved C-terminal (CCT) of human OSR1 Deposited 2021-05-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 423–527（105 aa） Chain B 423–527（105 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；Morpheus A8: 0.06 M Divalents 0.1 M Buffer System 2 7.5 37.5 % v/v Precipitant Mix 4. Divalents:Mg chloride; Ca chloride. Buffer: pH 7.5 Sodium HEPES; MOPS (acid). Precipitants: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350.	Resolution 1.62 Å R-free 0.216

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

View Construct and Data Evidence

UniProt name	OXSR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–290； UniProt 6–295 Author chain B； PDBConstruct 1–290； UniProt 6–295 Author chain C； PDBConstruct 1–290； UniProt 6–295 Author chain D； PDBConstruct 1–290； UniProt 6–295

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	3dak
Deposition date deposition_date	2008-05-29
Structure title title	Crystal Structure of Domain-Swapped OSR1 kinase domain
Keywords keywords	;SERINE/THREONINE PROTEIN KINASE, STE20, DOMAIN-SWAPPING, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide-binding, Phosphoprotein, Polymorphism, Serine/threonine-protein kinase, Transferase ;; TRANSFERASE
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	40.69 Å
Radius of gyration Rg (electron density) rg_electron	41.07 Å
Forward intensity I(0) i0	241619000.00
Molecular weight molecular_weight	127110.0 kDa
Excluded volume excluded_volume	159720 Å³
Envelope volume envelope_volume	219980 Å³
Hydration-shell volume shell_volume	48285 Å³
Envelope diameter envelope_diameter	146.3 Å
Shell Rg shell_rg	42.03 Å
Envelope Rg envelope_rg	40.68 Å
Shape Rg shape_rg	41.07 Å
Total Rg total_rg	41.10 Å
Total atoms total_atoms	8904
Residues n_residues	1122
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	143.9 Å
Rg (real space) rg_real	40.99 Å
Rg uncertainty (real space) rg_real_error	1.54 Å
I(0) (real space) i0_real	2.4160e+08
I(0) uncertainty (real space) i0_real_error	4.6320e+06
Rg (reciprocal space) rg_reciprocal	40.69 Å
I(0) (reciprocal space) i0_reciprocal	241500000.0000
Solution quality estimate total_estimate	0.7997
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	51.7 Å
Skewness Skewness skewness	0.591
Kurtosis Kurtosis kurtosis	-0.032
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34010000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.663; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.769; Smooth: 0.633

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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	Serine/threonine-protein kinase OSR1
Molecular weight formula_weight	32428.6 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9434

SALPWSINRDDYELQEVIGSGATAVVQAAYCAPKKEKVAIKRINLEKCQTSMDELLKEIQAMSQCHHPNIVSYYTSFVVKDELWLVMKLLSGGSVLDIIKHIVAKGEHKSGVLDESTIATILREVLEGLEYLHKNGQIHRDVKAGNILLGEDGSVQIADFGVSAFLATGGDITRNKVRKTFVGTPCWMAPEVMEQVRGYDFKADIWSFGITAIELATGAAPYHKYPPMKVLMLTLQNDPPSLETGVQDKEMLKKYGKSFRKMISLCLQKDPEKRPTAAELLRHKFFQKAK

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 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	530

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3daka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dakb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dakc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dakd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3dakA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dakA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dakB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dakB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dakC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dakC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dakD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dakD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	74.208 Å
Unit-cell length b length_b	104.484 Å
Unit-cell length c length_c	162.903 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	16

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

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1988
R_work r_work	0.1951
R_free r_free	0.2671

fit	/app/data/saxs_computation/da/3dak/3dak.fit
pddf	/app/data/pr_computation/da/3dak/3dak.pr.out
profile	/app/data/saxs_computation/da/3dak/3dak.dat

Crystal Structure of Domain-Swapped OSR1 kinase domain

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

Serine/threonine-protein kinase OSR1

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