SAXSdb — 4yl6

▼

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

Malcavernin

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 290–376	Fragment：truncated fragment of C-terminal adaptor domain, UNP residues 290-376	Mitogen-activated protein kinase kinase kinase 3 × 1 （Q99759）	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

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 4YL6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FQN Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD) Deposited 2012-06-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379) Chain B 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.072M ammonium sulfate, 0.2M potassium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.219
4FQN Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD) Deposited 2012-06-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.072M ammonium sulfate, 0.2M potassium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.219
4FQN Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD) Deposited 2012-06-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.072M ammonium sulfate, 0.2M potassium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.219
4TVQ CCM3 in complex with CCM2 LD-like motif Deposited 2014-06-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 224–239（16 aa） Fragment：INTERDOMAIN LINKER LD-LIKE MOTIF RESIDUES 224-239	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；15-20% PEG3350, 0.1-0.2M POTASSIUM FLUORIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K	Resolution 2.80 Å R-free 0.277
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
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 A 304–400（97 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
4YKC Crystal structure of cerebral cavernous malformation 2 C-terminal adaptor domain Deposited 2015-03-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–444（155 aa） Fragment：C-terminal adaptor domain, UNP residues 290-444	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 7；293 K；45% Tacsimate	Resolution 2.70 Å R-free 0.267
4YKD Crystal structure of truncated cerebral cavernous malformation 2 C-terminal adaptor domain Deposited 2015-03-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–376（87 aa） Fragment：truncated fragment of C-terminal adaptor domain, UNP residues 290-376	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 550, 50 mM calcium chloride	Resolution 1.93 Å R-free 0.235
9PVG Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3 Deposited 2025-08-01	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 A 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228) Chain D 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl pH 7, 20% PEG3350	Resolution 3.00 Å R-free 0.297
9PVG Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3 Deposited 2025-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228) Chain C 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl pH 7, 20% PEG3350	Resolution 3.00 Å R-free 0.297

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

View Construct and Data Evidence

UniProt name	CCM2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–88； UniProt 290–376

Mitogen-activated protein kinase kinase kinase 3

OrganismNot specified

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 1–22	Fragment：UNP residues 1-22	Malcavernin × 1 （Q9BSQ5）	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

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 4YL6	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
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 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 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

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 1–22； UniProt 1–22

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4yl6
Deposition date deposition_date	2015-03-05
Structure title title	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
Keywords keywords	adaptor-partner complex, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.84 Å
Radius of gyration Rg (electron density) rg_electron	13.10 Å
Forward intensity I(0) i0	3032720.00
Molecular weight molecular_weight	12195.0 kDa
Excluded volume excluded_volume	15303 Å³
Envelope volume envelope_volume	17079 Å³
Hydration-shell volume shell_volume	11162 Å³
Envelope diameter envelope_diameter	46.3 Å
Shell Rg shell_rg	18.78 Å
Envelope Rg envelope_rg	13.41 Å
Shape Rg shape_rg	13.08 Å
Total Rg total_rg	14.44 Å
Total atoms total_atoms	858
Residues n_residues	106
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	46.5 Å
Rg (real space) rg_real	14.71 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.0330e+06
I(0) uncertainty (real space) i0_real_error	3.3200e+04
Rg (reciprocal space) rg_reciprocal	14.73 Å
I(0) (reciprocal space) i0_reciprocal	3033000.0000
Solution quality estimate total_estimate	0.8717
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.017
Kurtosis Kurtosis kurtosis	-0.394
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	416200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.852

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Malcavernin
Molecular weight formula_weight	11302.8 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	928

MELSASATELLQDYMLTLRTKLSSQEIQQFAALLHEYRNGASIHEFCINLRQLYGDSRKFLLLGLRPFIPEKDSQHFENFLETIGVKDLEHHHHHH

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	Mitogen-activated protein kinase kinase kinase 3
Molecular weight formula_weight	2594.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDEQEALNSIMNDLVALQMNRR

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4yl6A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1160 — Paired amphipathic helix 2 (pah2 repeat)
Homologous superfamily homologous superfamily	20 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	61.210 Å
Unit-cell length b length_b	61.210 Å
Unit-cell length c length_c	68.980 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	45.780 Å
R factor r_factor	0.2049
R_work r_work	0.2033
R_free r_free	0.2372

fit	/app/data/saxs_computation/yl/4yl6/4yl6.fit
pddf	/app/data/pr_computation/yl/4yl6/4yl6.pr.out
profile	/app/data/saxs_computation/yl/4yl6/4yl6.dat

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

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

Malcavernin

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

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)