SAXSdb — 5fwu

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

KREMEN PROTEIN 1

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 29–373	Fragment：ECD, RESIDUES 29-373	CL CHLORIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；0.1 M NA3CITRATE, 1.0 M MGSO4, FINAL PH 5.6	Resolution 2.80 Å R-free 0.307

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 5FWU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FWS Wnt modulator Kremen crystal form I at 1.90A Deposited 2016-02-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–373（345 aa） Fragment：ECD, RESIDUES 29-373	Not recorded	SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2.0 M AMMONIUM SULFATE, 5 %V/V ISO-PROPANOL, pH 7.5	Resolution 1.90 Å R-free 0.227
5FWT Wnt modulator Kremen crystal form I at 2.10A Deposited 2016-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–373（345 aa） Fragment：ECD, RESIDUES 1-473	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1.000 M (NH4)H2PO4 0.100 M NA3CITRATE PH 5.6	Resolution 2.10 Å R-free 0.232
5FWV Wnt modulator Kremen crystal form III at 3.2A Deposited 2016-02-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–373（345 aa） Fragment：ECD, RESIDUES 29-373	Not recorded	CL CHLORIDE ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M HEPES/MOPS 7.5 30 % P550MME_P20K DRIED OUT	Resolution 3.20 Å R-free 0.265
5FWW Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) Deposited 2016-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 30–322（293 aa） Fragment：ECD, RESIDUES 30-322	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20 %W/V PEG3350 0.2 M NA/K-PHOSPHATE, pH 7.5	Resolution 3.50 Å R-free 0.355
6SNW Structure of Coxsackievirus A10 complexed with its receptor KREMEN1 Deposited 2019-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric	Chain E 23–375（353 aa）	Not recorded	SPH SPHINGOSINE × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 120	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9VFR Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1 Deposited 2025-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric	Chain G 30–322（293 aa）	Not recorded	STE STEARIC ACID × 60 MYR MYRISTIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 120	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
9VFR Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1 Deposited 2025-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 30–322（293 aa）	Not recorded	STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
9VFR Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1 Deposited 2025-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain G 30–322（293 aa）	Not recorded	STE STEARIC ACID × 5 MYR MYRISTIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
9VFR Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1 Deposited 2025-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain G 30–322（293 aa）	Not recorded	STE STEARIC ACID × 6 MYR MYRISTIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
9VFR Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1 Deposited 2025-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 30–322（293 aa）	Not recorded	STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KREM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 40–395； UniProt 29–373

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	5fwu
Deposition date deposition_date	2016-02-21
Structure title title	Wnt modulator Kremen crystal form II at 2.8A
Keywords keywords	SIGNALING PROTEIN, WNT, CELL SURFACE, SIGNALLING, MEMBRANE PROTEIN; SIGNALING 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	20.58 Å
Radius of gyration Rg (electron density) rg_electron	19.91 Å
Forward intensity I(0) i0	16793900.00
Molecular weight molecular_weight	30334.0 kDa
Excluded volume excluded_volume	37495 Å³
Envelope volume envelope_volume	43794 Å³
Hydration-shell volume shell_volume	18746 Å³
Envelope diameter envelope_diameter	63.0 Å
Shell Rg shell_rg	25.69 Å
Envelope Rg envelope_rg	20.01 Å
Shape Rg shape_rg	19.92 Å
Total Rg total_rg	20.63 Å
Total atoms total_atoms	2132
Residues n_residues	271
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	63.2 Å
Rg (real space) rg_real	20.50 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.6790e+07
I(0) uncertainty (real space) i0_real_error	1.8780e+05
Rg (reciprocal space) rg_reciprocal	20.52 Å
I(0) (reciprocal space) i0_reciprocal	16790000.0000
Solution quality estimate total_estimate	0.9146
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.153
Kurtosis Kurtosis kurtosis	-0.626
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3536000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.993

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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	KREMEN PROTEIN 1
Molecular weight formula_weight	44551.8 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	2132

MGILPSPGMPALLSLVSLLSVLLMGCVAETGAPSPGLGPGPECFTANGADYRGTQNWTALQGGKPCLFWNETFQHPYNTLKYPNGEGGLGEHNYCRNPDGDVSPWCYVAEHEDGVYWKYCEIPACQMPGNLGCYKDHGNPPPLTGTSKTSNKLTIQTCISFCRSQRFKFAGMESGYACFCGNNPDYWKYGEAASTECNSVCFGDHTQPCGGDGRIILFDTLVGACGGNYSAMSSVVYSPDFPDTYATGRVCYWTIRVPGASHIHFSFPLFDIRDSADMVELLDGYTHRVLARFHGRSRPPLSFNVSLDFVILYFFSDRINQAQGFAVLYQAVKEEGSENLYFQGGSLPQERPAVNQTVAEVITEQANLSVSAARSSKVLYVITTSPSHPPQTVPGTHHHHHHHHHH

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	HOMO SAPIENS

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5fwuA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

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8. Citations (1)

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Unit-cell length a length_a	65.780 Å
Unit-cell length b length_b	65.780 Å
Unit-cell length c length_c	75.014 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	4

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	65.780 Å
R factor r_factor	0.2200
R_work r_work	0.2157
R_free r_free	0.3071

fit	/app/data/saxs_computation/fw/5fwu/5fwu.fit
pddf	/app/data/pr_computation/fw/5fwu/5fwu.pr.out
profile	/app/data/saxs_computation/fw/5fwu/5fwu.dat

Wnt modulator Kremen crystal form II at 2.8A

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

KREMEN PROTEIN 1

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