SAXSdb — 2i04

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

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1

Mus musculus

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 463–546 Chain B； UniProt 463–546	Fragment：PDZ1 domain	peptide E6 × 2 （P06463） SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.6；291 K；PEG2000, 0.1 M Na Acetate , pH 4.6, VAPOR DIFFUSION, temperature 291K	Resolution 2.15 Å R-free 0.269

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 2I04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5ZYS Structure of Nephrin/MAGI1 complex Deposited 2018-05-28	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 826–918（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.5M sodium chloride , 0.01M magnesium chloride hexahydrate , 0.01Mhexadecyltrimethylammonium bromide	Resolution 1.78 Å R-free 0.204

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAGI1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–85； UniProt 463–546 Author chain B； PDBConstruct 2–85； UniProt 463–546

peptide E6

OrganismNot specified

UniProt P06463

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 152–158 Chain D； UniProt 152–158	Not recorded	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 × 2 （Q6RHR9） SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.6；291 K；PEG2000, 0.1 M Na Acetate , pH 4.6, VAPOR DIFFUSION, temperature 291K	Resolution 2.15 Å R-free 0.269

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 2I04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2I0I X-ray crystal structure of Sap97 PDZ3 bound to the C-terminal peptide of HPV18 E6 Deposited 2006-08-10	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 D 152–158（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG4000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 291K	Resolution 2.80 Å R-free 0.289
2I0I X-ray crystal structure of Sap97 PDZ3 bound to the C-terminal peptide of HPV18 E6 Deposited 2006-08-10	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 E 152–158（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG4000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 291K	Resolution 2.80 Å R-free 0.289
2I0I X-ray crystal structure of Sap97 PDZ3 bound to the C-terminal peptide of HPV18 E6 Deposited 2006-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 152–158（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG4000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 291K	Resolution 2.80 Å R-free 0.289
2I0L X-ray crystal structure of Sap97 PDZ2 bound to the C-terminal peptide of HPV18 E6. Deposited 2006-08-10	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 C 152–158（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；291 K；2M Ammonium Sulfate, 0.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, temperature 291K	Resolution 2.31 Å R-free 0.302
2I0L X-ray crystal structure of Sap97 PDZ2 bound to the C-terminal peptide of HPV18 E6. Deposited 2006-08-10	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 D 152–158（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；291 K；2M Ammonium Sulfate, 0.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, temperature 291K	Resolution 2.31 Å R-free 0.302
4JOR CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncoprotein C-terminal peptide (RLQRRRETQV) Deposited 2013-03-18	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 C 149–158（10 aa） Fragment：HPV18 E6 peptide	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；29% (w/v) polyethylene glycol (PEG), 0.075 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.34 Å R-free 0.181
4JOR CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncoprotein C-terminal peptide (RLQRRRETQV) Deposited 2013-03-18	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 D 149–158（10 aa） Fragment：HPV18 E6 peptide	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；29% (w/v) polyethylene glycol (PEG), 0.075 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.34 Å R-free 0.181
5K4F CAL PDZ mutant C319A with a peptide Deposited 2016-05-20	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 C 149–158（10 aa） Fragment：UNP residues 149-158	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；31% PEG3350, 125mM NaCl, 0.1M Tris7.5	Resolution 1.36 Å R-free 0.183
5K4F CAL PDZ mutant C319A with a peptide Deposited 2016-05-20	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 D 149–158（10 aa） Fragment：UNP residues 149-158	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；31% PEG3350, 125mM NaCl, 0.1M Tris7.5	Resolution 1.36 Å R-free 0.183
6SJV Structure of HPV18 E6 oncoprotein in complex with mutant E6AP LxxLL motif Deposited 2019-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa）	Mutation：;K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R,K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R,K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R ;	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；Sodium Cacodylate 100 mM pH 6.5, PEG 8000 5%, 2-methyl-2,4-pentanediol 40%	Resolution 2.03 Å R-free 0.242
6ZFD 14-3-3 zeta bound to the phosphorylated 18E6 C-terminus Deposited 2020-06-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 152–158（7 aa） Chain B 152–158（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；19% PEG4000, 0.1M cacodylate, 20%glycerol as a cryoprotectant	Resolution 1.90 Å R-free 0.207
6ZFG 14-3-3 zeta chimera with 18E6 and fusicoccin Deposited 2020-06-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 152–158（7 aa） Chain B 152–158（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 FSC FUSICOCCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；19% PEG4000, 0.1M cacodylate, 20%glycerol as a cryoprotectant	Resolution 1.85 Å R-free 0.219
8B82 Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide Deposited 2022-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 149–158（10 aa） Chain D 149–158（10 aa）	Not recorded	CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；15% PEG 4000, 0.05 M Ammonium Sulfate	Resolution 2.80 Å R-free 0.278
8OEP Crystal structure of the PTPN3 PDZ domain bound to the HPV18 E6 oncoprotein C-terminal peptide Deposited 2023-03-11	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 146–158（13 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% w/v PEG 3350, 0.2 M NaI at pH 7;	Resolution 1.87 Å R-free 0.249
8OEP Crystal structure of the PTPN3 PDZ domain bound to the HPV18 E6 oncoprotein C-terminal peptide Deposited 2023-03-11	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 D 146–158（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% w/v PEG 3350, 0.2 M NaI at pH 7;	Resolution 1.87 Å R-free 0.249

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VE6_HPV18
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–7； UniProt 152–158 Author chain D； PDBConstruct 1–7； UniProt 152–158

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	2i04
Deposition date deposition_date	2006-08-09
Structure title title	X-ray crystal structure of MAGI-1 PDZ1 bound to the C-terminal peptide of HPV18 E6
Keywords keywords	PDZ, E6 binding, tumor suppressor, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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	18.45 Å
Radius of gyration Rg (electron density) rg_electron	17.60 Å
Forward intensity I(0) i0	7601260.00
Molecular weight molecular_weight	19774.0 kDa
Excluded volume excluded_volume	24616 Å³
Envelope volume envelope_volume	28447 Å³
Hydration-shell volume shell_volume	14394 Å³
Envelope diameter envelope_diameter	62.5 Å
Shell Rg shell_rg	22.64 Å
Envelope Rg envelope_rg	17.86 Å
Shape Rg shape_rg	17.55 Å
Total Rg total_rg	18.55 Å
Total atoms total_atoms	1384
Residues n_residues	182
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	62.8 Å
Rg (real space) rg_real	18.52 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	7.6010e+06
I(0) uncertainty (real space) i0_real_error	1.0650e+05
Rg (reciprocal space) rg_reciprocal	18.51 Å
I(0) (reciprocal space) i0_reciprocal	7601000.0000
Solution quality estimate total_estimate	0.7760
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.0 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	-0.127
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1823000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.708; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; 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	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Molecular weight formula_weight	9076.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1608

SIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	peptide E6
Molecular weight formula_weight	947.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

RRRETQV

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2i04A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2i04B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (2)

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Unit-cell length a length_a	48.961 Å
Unit-cell length b length_b	27.611 Å
Unit-cell length c length_c	59.525 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	28.690 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2690

fit	/app/data/saxs_computation/i0/2i04/2i04.fit
pddf	/app/data/pr_computation/i0/2i04/2i04.pr.out
profile	/app/data/saxs_computation/i0/2i04/2i04.dat

X-ray crystal structure of MAGI-1 PDZ1 bound to the C-terminal peptide of HPV18 E6

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

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

peptide E6

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)