5UB5
human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP
- PDB DOI: https://doi.org/10.2210/pdb5UB5/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens, Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2016-12-20 Released: 2017-08-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.193
- R-Value Work: 0.153
- R-Value Observed: 0.155
This is version 1.4 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 |
| Protein O-glucosyltransferase 1 | 357 | Homo sapiens | Mutation(s): 0 Gene Names: POGLUT1, C3orf9, CLP46, KTELC1, MDSRP, MDS010, UNQ490/PRO1006 EC: 2.4.1 (PDB Primary Data), 2.4.2.26 (PDB Primary Data) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8NBL1 (Homo sapiens) Explore Q8NBL1 Go to UniProtKB: Q8NBL1 | |||||
PHAROS: Q8NBL1 GTEx: ENSG00000163389 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8NBL1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Neurogenic locus notch homolog protein 1 | 42 | Homo sapiens | Mutation(s): 1 Gene Names: NOTCH1, TAN1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P46531 (Homo sapiens) Explore P46531 Go to UniProtKB: P46531 | |||||
PHAROS: P46531 GTEx: ENSG00000148400 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P46531 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UDP Query on UDP | F [auth A] | URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N |  | ||
| NAG Query on NAG | C [auth A], D [auth A], E [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| CA Query on CA | G [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.193
- R-Value Work: 0.153
- R-Value Observed: 0.155
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.951 | α = 90 |
| b = 74.072 | β = 90 |
| c = 83.583 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| SAINT | data scaling |
| PDB_EXTRACT | data extraction |
| SAINT | data reduction |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-08-09 Deposition Author(s): Li, Z., Rini, J.M.
Revision History (Full details and data files)
- Version 1.0: 2017-08-09
Type: Initial release - Version 1.1: 2017-08-30
Changes: Database references - Version 1.2: 2018-04-04
Changes: Data collection, Source and taxonomy - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
