SAXSdb — 2o2v

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

Dual specificity mitogen-activated protein kinase kinase 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 5–108	Fragment：MAP2K5-phox	Mitogen-activated protein kinase kinase kinase 3 × 1 （Q99759）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.02M CaCl2, 0.1M Na(CH3COO), 30% MPD, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.83 Å R-free 0.224

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 2O2V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NPT Crystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox domain (MAP2K5-phox) with human mitogen activated protein kinase kinase kinase 2 phox domain (MAP3K2-phox) Deposited 2006-10-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–108（104 aa） Fragment：MAP2K5-phox	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M NH4(CH3COO), 0.1M TRIS, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.247
2NPT Crystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox domain (MAP2K5-phox) with human mitogen activated protein kinase kinase kinase 2 phox domain (MAP3K2-phox) Deposited 2006-10-30	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 5–108（104 aa） Fragment：MAP2K5-phox	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M NH4(CH3COO), 0.1M TRIS, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.247
4IC7 Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment Deposited 2012-12-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 16–130（115 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 16–130（115 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

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

View Construct and Data Evidence

UniProt name	MP2K5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–106； UniProt 5–108

Mitogen-activated protein kinase kinase kinase 3

Homo sapiens

UniProt Q99759

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 37–124	Fragment：MAP3K3B-phox	Dual specificity mitogen-activated protein kinase kinase 5 × 1 （Q13163）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.02M CaCl2, 0.1M Na(CH3COO), 30% MPD, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.83 Å R-free 0.224

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 2O2V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2C60 crystal structure of human mitogen-activated protein kinase kinase kinase 3 isoform 2 phox domain at 1.25 A resolution Deposited 2005-11-04	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 37–124（88 aa） Fragment：PHOX DOMAIN, RESIDUES 37-124	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；150 NANOLITRE SITTING DROPS, 0.2 KSCN, 20% PEG3350, 10% ETHYLENE GLYCOL	Resolution 1.25 Å R-free 0.182
2JRH Solution structure of human MEKK3 PB1 domain cis isomer Deposited 2007-06-26	Different construct 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 42–126（85 aa） Fragment：OPR, PB1 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Pressure 1 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] MEKK3 PB1-cis, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 15N] MEKK3 PB1-cis, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2PPH solution structure of human MEKK3 PB1 domain Deposited 2007-04-30	Different construct 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 42–126（85 aa） Fragment：PB1 domain (Residues 42-126)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Pressure 1 NMR sample composition 0.5mM 15N,13C-labeled MEKK3 PB1 50mM phosphate buffer (pH 6.0), 1mM EDTA,10%(v/v) D2O \| 90% H2O/10% D2O	Resolution not provided
4Y5O CCM2 HHD in complex with MEKK3 NPB1 Deposited 2015-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–124（124 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M potassium phosphate and 20% PEG 3350	Resolution 2.35 Å R-free 0.232
4YL6 Crystal structure of truncated cerebral cavernous malformation 2 C-terminal adaptor domain in complex with an internal helix of mitogen-activated protein kinase kinase kinase 3 Deposited 2015-03-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–22（22 aa） Fragment：UNP residues 1-22	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；3.5 M Sodium Formate	Resolution 2.10 Å R-free 0.237

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	M3K3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–90； UniProt 37–124

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	2o2v
Deposition date deposition_date	2006-11-30
Structure title title	Crystal Structure of the Complex of Human Mitogen Activated Protein Kinase Kinase 5 Phox Domain (MAP2K5-phox) with Human Mitogen Activated Protein Kinase Kinase Kinase 3 (MAP3K3B-phox)
Keywords keywords	;mitogen activated protein kinase kinase 5, MAP2K5, MEK5, MKK5, PRKMK5, MAP kinase 5, phox, phox-domain, mitogen activated protein kinase kinase kinase 3, MEKK3, MAPKKK3, MAP/ERK kinase kinase 3, Structural Genomics, Structural Genomics Consortium, SGC, 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	18.07 Å
Radius of gyration Rg (electron density) rg_electron	17.07 Å
Forward intensity I(0) i0	6834260.00
Molecular weight molecular_weight	19430.0 kDa
Excluded volume excluded_volume	24475 Å³
Envelope volume envelope_volume	29272 Å³
Hydration-shell volume shell_volume	14815 Å³
Envelope diameter envelope_diameter	58.9 Å
Shell Rg shell_rg	22.48 Å
Envelope Rg envelope_rg	17.34 Å
Shape Rg shape_rg	17.07 Å
Total Rg total_rg	18.01 Å
Total atoms total_atoms	1371
Residues n_residues	174
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	59.2 Å
Rg (real space) rg_real	18.02 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	6.8340e+06
I(0) uncertainty (real space) i0_real_error	8.0610e+04
Rg (reciprocal space) rg_reciprocal	18.02 Å
I(0) (reciprocal space) i0_reciprocal	6834000.0000
Solution quality estimate total_estimate	0.7404
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.8 Å
Skewness Skewness skewness	0.266
Kurtosis Kurtosis kurtosis	-0.385
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1764000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 0.408; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

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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	Dual specificity mitogen-activated protein kinase kinase 5
Molecular weight formula_weight	11941.5 kDa
EC 编号 ec_number	2.7.12.2
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	1520

SMALGPFPAMENQVLVIRIKIPNSGAVDWTVHSGPQLLFRDVLDVIGQVLPEATTTAFEYEDEDGDRITVRSDEEMKAMLSYYYSTVMEQQVNGQLIEPLQIFPRA

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	Mitogen-activated protein kinase kinase kinase 3
Molecular weight formula_weight	10484.9 kDa
EC 编号 ec_number	2.7.11.25
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SMGHSNRQSDVRIKFEHNGERRIIAFSRPVKYEDVEHKVTTVFGQPLDLHYMNNELSILLKNQDDLDKAIDILDRSSSMKSLRILLLSQD

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2o2va_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.2 — CAD & PB1 domains
Family Family family	d.15.2.2 — PB1 domain

Domain ID domain_id	d2o2vb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.2 — CAD & PB1 domains
Family Family family	d.15.2.2 — PB1 domain

CATH v4.4 (2 domains)

Domain ID domain_id	2o2vA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2o2vB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	87.654 Å
Unit-cell length b length_b	87.654 Å
Unit-cell length c length_c	55.408 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	1.830 Å
Low-resolution limit resolution_low	46.830 Å
R factor r_factor	0.1960
R_work r_work	0.1940
R_free r_free	0.2240

fit	/app/data/saxs_computation/o2/2o2v/2o2v.fit
pddf	/app/data/pr_computation/o2/2o2v/2o2v.pr.out
profile	/app/data/saxs_computation/o2/2o2v/2o2v.dat

Crystal Structure of the Complex of Human Mitogen Activated Protein Kinase Kinase 5 Phox Domain (MAP2K5-phox) with Human Mitogen Activated Protein Kinase Kinase Kinase 3 (MAP3K3B-phox)

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

Dual specificity mitogen-activated protein kinase kinase 5

State in the Current Structure

Other States of the Same Protein in the Database

Mitogen-activated protein kinase kinase kinase 3

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

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)