Download MendeleyGLMP is essential for bone-marrow hematopoiesis and lysosomal glycolipid metabolism
Manzanillo, P., Huang, C.S., Boenig, G., Calses, P., Scherl, A., Reichelt, M., Katakam, A.K., Martin, F., Hymowitz, S.G., Ouyang, W.To be published.
6NYQ
Crystal structure of glycosylated lysosomal membrane protein (GLMP) luminal domain bound to a Fab fragment
- PDB DOI: https://doi.org/10.2210/pdb6NYQ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Escherichia coli, Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2019-02-12 Released: 2020-01-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.204
- R-Value Work: 0.164
- R-Value Observed: 0.166
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 1H3 Fab light chain | A [auth L] | 214 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 |
| 1H3 Fab heavy chain | B [auth H] | 227 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glycosylated lysosomal membrane protein | 404 | Mus musculus | Mutation(s): 0 Gene Names: Glmp |  | |
UniProt | |||||
Find proteins for Q9JHJ3 (Mus musculus) Explore Q9JHJ3 Go to UniProtKB: Q9JHJ3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9JHJ3 | ||||
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 | H [auth C] I [auth C] J [auth C] K [auth C] L [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| NA Query on NA | D [auth H], E [auth C], F [auth C], G [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.204
- R-Value Work: 0.164
- R-Value Observed: 0.166
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.924 | α = 90 |
| b = 55.238 | β = 99.35 |
| c = 99.639 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2020-01-22 Deposition Author(s): Huang, C.S., Boenig, G., Hymowitz, S.G.
Revision History (Full details and data files)
- Version 1.0: 2020-01-22
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2024-11-20
Changes: Data collection, Database references, Structure summary
