SAXSdb — 5byz

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

Mitogen-activated protein kinase 7

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 48–395	Fragment：KINASE DOMAIN, unp residues 48-395	4WE 4-({5-fluoro-4-[2-methyl-1-(propan-2-yl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)-N-[2-(piperidin-1-yl)ethyl]benzamide × 1 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；11 % PEG4000 0.01 M MgCl2 0.18 M Na-Formiate 0.10 M MES, pH=6.50 0.01 M Tris/Cl, pH=8.50	Resolution 1.65 Å R-free 0.192

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 5BYZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Q8Y Structural insight into the enzymatic mechanism of the phophothreonine lyase Deposited 2007-06-12	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 B 214–222（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；12% PEG3350,0.1M MES pH6.0,0.1 M NaKTartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.217
4B99 Crystal Structure of MAPK7 (ERK5) with inhibitor Deposited 2012-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–397（397 aa） Fragment：KINASE DOMAIN	Not recorded	R4L 11-cyclopentyl-2-[[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl-phenyl]amino]-5-methyl-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.05M CACL2, 0.1M MES PH 6.0, 20% PEG 6000, 10% ETHYLENE GLYCOL	Resolution 2.80 Å R-free 0.287
4IC7 Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment Deposited 2012-12-10	Different construct 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 1–431（431 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；48% PEG 200, 100mM MIB, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.60 Å R-free 0.258
4IC7 Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment Deposited 2012-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–431（431 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；48% PEG 200, 100mM MIB, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.60 Å R-free 0.258
4IC8 Crystal structure of the apo ERK5 kinase domain Deposited 2012-12-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–431（431 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；296 K；30% PEG 200, 100mM MIB, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.80 Å R-free 0.290
4IC8 Crystal structure of the apo ERK5 kinase domain Deposited 2012-12-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–431（431 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；296 K；30% PEG 200, 100mM MIB, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.80 Å R-free 0.290
4ZSG MITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR Deposited 2015-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 47–393（347 aa） Fragment：residues 47-393	Not recorded	GOL GLYCEROL × 5 4QX 3-amino-5-[(4-chlorophenyl)amino]-N-(propan-2-yl)-1H-1,2,4-triazole-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；4-6 % w/v PEG 6000, 0.1 M MES, 5 mM DTT	Resolution 1.79 Å R-free 0.235
4ZSJ MITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR Deposited 2015-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–393（344 aa） Fragment：UNP residues 50-393	Not recorded	GOL GLYCEROL × 4 4R0 3-amino-5-[(4-chloro-3-methylphenyl)amino]-N-(propan-2-yl)-1H-1,2,4-triazole-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；4-6 % w/v PEG 6000, 0.1 M MES, 5 mM DTT	Resolution 2.48 Å R-free 0.230
4ZSL MITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR Deposited 2015-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 53–393（341 aa） Fragment：UNP residues 53-393	Not recorded	4QZ 3-amino-5-[(4-chlorophenyl)amino]-N-[(1S)-1-phenylethyl]-1H-1,2,4-triazole-1-carboxamide × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；297 K；4-6 % w/v PEG 6000, 0.1 M MES, 5 mM DTT	Resolution 2.25 Å R-free 0.219
5BYY ERK5 IN COMPLEX WITH SMALL MOLECULE Deposited 2015-06-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–394（346 aa） Fragment：KINASE DOMAIN, unp residues 49-394	Not recorded	4WG 2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.01 M Tris 8.50 0.01 M MgCl2 13 % PEG4000 0.18 M Na-formiate 0.10 M MES, pH=6.50	Resolution 2.79 Å R-free 0.273
5O7I ERK5 in complex with a pyrrole inhibitor Deposited 2017-06-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 46–402（357 aa） Fragment：UNP residues 46-402	Not recorded	9N8 4-(2-bromanyl-6-fluoranyl-phenyl)carbonyl-~{N}-pyridin-3-yl-1~{H}-pyrrole-2-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；5 % (v/v) PEG 6000, 0.1 M MES (pH 6.0), 5 mM DTT	Resolution 2.38 Å R-free 0.220
6HKM Crystal structure of Compound 1 with ERK5 Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–395（347 aa） Fragment：KINASE DOMAIN	Not recorded	G92 [4-(6,7-dimethoxyquinazolin-4-yl)piperidin-1-yl]-[4-(trifluoromethyloxy)phenyl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；11% PEG 4000, 100mM MgCl2, 160mM sodium formate, 100mM MES pH 6.75, 10mM Tris pH 8.5	Resolution 2.47 Å R-free 0.280
6HKN Crystal structure of Compound 35 with ERK5 Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–393（340 aa） Fragment：KINASE DOMAIN	Not recorded	G9E [2-azanyl-4-(trifluoromethyloxy)phenyl]-[4-(7-methoxyquinazolin-4-yl)piperidin-1-yl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG 4000, 100mM MgCl2, 180mM Sodium formate, 100 mM MES pH 6.5, 10mM Tris pH 8.0	Resolution 2.33 Å R-free 0.249
7PUS ERK5 in complex with Pyrrole Carboxamide scaffold Deposited 2021-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 46–402（357 aa） Fragment：UNP residues 46-402	Not recorded	86E 4-[3,6-bis(chloranyl)-2-fluoranyl-phenyl]carbonyl-~{N}-(1-methylpyrazol-4-yl)-1~{H}-pyrrole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5 % (V/V) PEG 6000, 0.1 M MES (PH 6.0), 5 MM DTT	Resolution 2.59 Å R-free 0.285
9LTA Crystal Structure of Compound SKLB-D18 with MAPK7 (ERK5) Deposited 2025-02-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 48–393（346 aa）	Not recorded	A1EKR 4-[5-chloranyl-2-[[3-[(dimethylamino)methyl]phenyl]amino]pyrimidin-4-yl]-~{N}-morpholin-4-yl-thiophene-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Hepes 7.5, 10% PEG4K, 7% isopropanol	Resolution 2.33 Å R-free 0.292
9LTA Crystal Structure of Compound SKLB-D18 with MAPK7 (ERK5) Deposited 2025-02-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 48–393（346 aa）	Not recorded	A1EKR 4-[5-chloranyl-2-[[3-[(dimethylamino)methyl]phenyl]amino]pyrimidin-4-yl]-~{N}-morpholin-4-yl-thiophene-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Hepes 7.5, 10% PEG4K, 7% isopropanol	Resolution 2.33 Å R-free 0.292

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MK07_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–348； UniProt 48–395

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	5byz
Deposition date deposition_date	2015-06-11
Structure title title	ERK5 in complex with small molecule
Keywords keywords	ERk5, kinase inhibitor, 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	22.24 Å
Radius of gyration Rg (electron density) rg_electron	21.18 Å
Forward intensity I(0) i0	27279800.00
Molecular weight molecular_weight	40773.0 kDa
Excluded volume excluded_volume	51416 Å³
Envelope volume envelope_volume	60435 Å³
Hydration-shell volume shell_volume	23693 Å³
Envelope diameter envelope_diameter	74.8 Å
Shell Rg shell_rg	28.15 Å
Envelope Rg envelope_rg	21.50 Å
Shape Rg shape_rg	21.17 Å
Total Rg total_rg	22.08 Å
Total atoms total_atoms	2874
Residues n_residues	348
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	72.1 Å
Rg (real space) rg_real	22.18 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	2.7280e+07
I(0) uncertainty (real space) i0_real_error	3.7670e+05
Rg (reciprocal space) rg_reciprocal	22.20 Å
I(0) (reciprocal space) i0_reciprocal	27280000.0000
Solution quality estimate total_estimate	0.6236
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.312
Kurtosis Kurtosis kurtosis	-0.248
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6598000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 0.999; Sysdev: 0.189; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	Mitogen-activated protein kinase 7
Molecular weight formula_weight	39826.9 kDa
EC 编号 ec_number	2.7.11.24
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	3367

TFDVGDEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARREGI

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	4-({5-fluoro-4-[2-methyl-1-(propan-2-yl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)-N-[2-(piperidin-1-yl)ethyl]benzamide
Molecular weight formula_weight	465.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	336

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5byza_
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 (2 domains)

Domain ID domain_id	5byzA01
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	5byzA02
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	93.401 Å
Unit-cell length b length_b	93.401 Å
Unit-cell length c length_c	116.280 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	72.820 Å
R factor r_factor	0.1747
R_work r_work	0.1737
R_free r_free	0.1923

fit	/app/data/saxs_computation/by/5byz/5byz.fit
pddf	/app/data/pr_computation/by/5byz/5byz.pr.out
profile	/app/data/saxs_computation/by/5byz/5byz.dat

ERK5 in complex with small molecule

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

Mitogen-activated protein kinase 7

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