6H15
Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-B10
- PDB DOI: https://doi.org/10.2210/pdb6H15/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens, Lama glama
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): No 
- Deposited: 2018-07-11 Released: 2019-01-30 
- Funding Organization(s): Netherlands Organisation for Scientific Research
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.247 
- R-Value Work: 0.198 
- R-Value Observed: 0.201 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Low-density lipoprotein receptor-related protein 6 | A, D [auth B] | 616 | Homo sapiens | Mutation(s): 0  Gene Names: LRP6 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75581 (Homo sapiens) Explore O75581  Go to UniProtKB:  O75581 | |||||
PHAROS:  O75581 GTEx:  ENSG00000070018  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O75581 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
VHH L-P2-B10 | B [auth C], C [auth D] | 123 | Lama glama | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, G | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F, I | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | H | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | M [auth A] N [auth A] O [auth C] P [auth C] S [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.247 
- R-Value Work: 0.198 
- R-Value Observed: 0.201 
- Space Group: P 65
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 118.314 | α = 90 |
b = 118.314 | β = 90 |
c = 249.951 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-01-30  Deposition Author(s): Gros, P., van Scherpenzeel, R.C.
Funding Organization | Location | Grant Number |
---|---|---|
Netherlands Organisation for Scientific Research | Netherlands | 01.80.104.00 |
Revision History (Full details and data files)
- Version 1.0: 2019-01-30
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary