4KNG
Crystal structure of human LGR5-RSPO1-RNF43
- PDB DOI: https://doi.org/10.2210/pdb4KNG/pdb
- Classification: Signaling Protein, Membrane Protein
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2013-05-09 Released: 2013-06-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.276 
- R-Value Work: 0.232 
- R-Value Observed: 0.234 
This is version 1.3 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 |
Leucine-rich repeat-containing G-protein coupled receptor 5 | 531 | Homo sapiens | Mutation(s): 0  Gene Names: LGR5, GPR49, GPR67 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75473 (Homo sapiens) Explore O75473  Go to UniProtKB:  O75473 | |||||
PHAROS:  O75473 GTEx:  ENSG00000139292  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O75473 | ||||
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 |
R-spondin-1 | C [auth M], D [auth P] | 115 | Homo sapiens | Mutation(s): 0  Gene Names: RSPO1 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q2MKA7 (Homo sapiens) Explore Q2MKA7  Go to UniProtKB:  Q2MKA7 | |||||
PHAROS:  Q2MKA7 GTEx:  ENSG00000169218  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q2MKA7 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
E3 ubiquitin-protein ligase RNF43 | 160 | Homo sapiens | Mutation(s): 0  Gene Names: RNF43 EC: 6.3.2 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q68DV7 (Homo sapiens) Explore Q68DV7  Go to UniProtKB:  Q68DV7 | |||||
PHAROS:  Q68DV7 GTEx:  ENSG00000108375  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q68DV7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A], I [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
NI Query on NI | H [auth B] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.276 
- R-Value Work: 0.232 
- R-Value Observed: 0.234 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 104.575 | α = 90 |
b = 120.971 | β = 90 |
c = 181.009 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-3000 | data collection |
X-PLOR | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
SCALA | data scaling |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 2013-06-19  Deposition Author(s): Chen, P.H., He, X.
Revision History (Full details and data files)
- Version 1.0: 2013-06-19
Type: Initial release - Version 1.1: 2013-07-03
Changes: Data collection - Version 1.2: 2013-07-24
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary