5fww

Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4)

Method: X-RAY DIFFRACTION Dmax: 119.2 Å Quality: GOOD

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

LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6

HOMO SAPIENS

UniProt O75581

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 630–1246 Fragment:PE3PE4, RESIDUES 630-1246 KREMEN PROTEIN 1 × 1 (Q96MU8) DICKKOPF-RELATED PROTEIN 1 × 1 (O94907) 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

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.

27 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LRP6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–619; UniProt 630–1246

KREMEN PROTEIN 1

HOMO SAPIENS

UniProt Q96MU8

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 30–322 Fragment:ECD, RESIDUES 30-322 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6 × 1 (O75581) DICKKOPF-RELATED PROTEIN 1 × 1 (O94907) 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

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.

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 2
Chains and sequence ranges Author chain B; PDBConstruct 1–293; UniProt 30–322

DICKKOPF-RELATED PROTEIN 1

HOMO SAPIENS

UniProt O94907

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 182–266 Fragment:CRD2, RESIDUES 182-266 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6 × 1 (O75581) KREMEN PROTEIN 1 × 1 (Q96MU8) 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

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.

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

View Construct and Data Evidence
UniProt name DKK1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–85; UniProt 182–266

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5fww

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5fww
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5fww
Deposition date deposition_date2016-02-21
Structure title titleWnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4)
Keywords keywordsSIGNALING PROTEIN, WNT, CELL SURFACE, SIGNALLING, MEMBRANE PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.16
Radius of gyration Rg (electron density) rg_electron34.88
Forward intensity I(0) i0199018000.00
Molecular weight molecular_weight110010.0 kDa
Excluded volume excluded_volume136160 ų
Envelope volume envelope_volume177120 ų
Hydration-shell volume shell_volume42849 ų
Envelope diameter envelope_diameter122.2
Shell Rg shell_rg40.47
Envelope Rg envelope_rg34.78
Shape Rg shape_rg34.88
Total Rg total_rg35.26
Total atoms total_atoms7730
Residues n_residues976
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax119.2
Rg (real space) rg_real35.23
Rg uncertainty (real space) rg_real_error1.19
I(0) (real space) i0_real1.9900e+08
I(0) uncertainty (real space) i0_real_error3.2080e+06
Rg (reciprocal space) rg_reciprocal35.19
I(0) (reciprocal space) i0_reciprocal199000000.0000
Solution quality estimate total_estimate0.8798
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.4
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.444
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35240000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.917

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5fwwA01
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily30 — TolB, C-terminal domain
Domain ID domain_id5fwwA02
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily30 — TolB, C-terminal domain
Domain ID domain_id5fwwB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily10 — Plasminogen Kringle 4
Domain ID domain_id5fwwC00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology80 — Lipase, subunit A
Homologous superfamily homologous superfamily10 — Lipase, subunit A

8. Citations (1)

9. Files and Curves (10)