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
