SAXSdb — 2c60

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

HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3 ISOFORM 2

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 37–124	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

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 2C60	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JRH Solution structure of human MEKK3 PB1 domain cis isomer Deposited 2007-06-26	Different construct Different mutation/modification 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 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
2O2V 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) Deposited 2006-11-30	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 37–124（88 aa） Fragment：MAP3K3B-phox	Not recorded	No recorded non-water small molecule	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
2PPH solution structure of human MEKK3 PB1 domain Deposited 2007-04-30	Different construct Different mutation/modification 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 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 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 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 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 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–111； 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	2c60
Deposition date deposition_date	2005-11-04
Structure title title	crystal structure of human mitogen-activated protein kinase kinase kinase 3 isoform 2 phox domain at 1.25 A resolution
Keywords keywords	;MAP3K3, MAP/ERK KINASE KINASE 3, MAPKKK3, MEKK3, SERINE THREONINE PHOSPHORYLATION, ATP-BINDING, KINASE, MAGNESIUM, METAL-BINDING, NUCLEOTIDE-BINDING, PHOSPHORYLATION, 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	13.96 Å
Radius of gyration Rg (electron density) rg_electron	12.42 Å
Forward intensity I(0) i0	2107820.00
Molecular weight molecular_weight	9828.0 kDa
Excluded volume excluded_volume	12268 Å³
Envelope volume envelope_volume	14269 Å³
Hydration-shell volume shell_volume	9972 Å³
Envelope diameter envelope_diameter	47.3 Å
Shell Rg shell_rg	17.85 Å
Envelope Rg envelope_rg	12.87 Å
Shape Rg shape_rg	12.41 Å
Total Rg total_rg	13.76 Å
Total atoms total_atoms	683
Residues n_residues	83
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	48.5 Å
Rg (real space) rg_real	13.87 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	2.1080e+06
I(0) uncertainty (real space) i0_real_error	2.2880e+04
Rg (reciprocal space) rg_reciprocal	13.87 Å
I(0) (reciprocal space) i0_reciprocal	2108000.0000
Solution quality estimate total_estimate	0.8467
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.8 Å
Skewness Skewness skewness	0.110
Kurtosis Kurtosis kurtosis	-0.250
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	300900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

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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	HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3 ISOFORM 2
Molecular weight formula_weight	13144.1 kDa
EC 编号 ec_number	2.7.1.37
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	844

MHHHHHHSSGVDLGTENLYFQSMGHSNRQSDVRIKFEHNGERRIIAFSRPVKYEDVEHKVTTVFGQPLDLHYMNNELSILLKNQDDLDKAIDILDRSSSMKSLRILLLSQD

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 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2c60a1
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	d2c60a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2c60A01
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	82.800 Å
Unit-cell length b length_b	42.300 Å
Unit-cell length c length_c	30.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	39.720 Å
R factor r_factor	0.1660
R_work r_work	0.1650
R_free r_free	0.1820

fit	/app/data/saxs_computation/c6/2c60/2c60.fit
pddf	/app/data/pr_computation/c6/2c60/2c60.pr.out
profile	/app/data/saxs_computation/c6/2c60/2c60.dat

crystal structure of human mitogen-activated protein kinase kinase kinase 3 isoform 2 phox domain at 1.25 A resolution

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

HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3 ISOFORM 2

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