5HGV
Structure of an O-GlcNAc transferase point mutant, D554N in complex with peptide
- PDB DOI: https://doi.org/10.2210/pdb5HGV/pdb
- Classification: TRANSFERASE/PEPTIDE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2016-01-08 Released: 2016-09-14
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.237
- R-Value Work: 0.217
- R-Value Observed: 0.218
This is version 1.5 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 |
| UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | 719 | Homo sapiens | Mutation(s): 1 Gene Names: OGT EC: 2.4.1.255 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O15294 (Homo sapiens) Explore O15294 Go to UniProtKB: O15294 | |||||
PHAROS: O15294 GTEx: ENSG00000147162 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O15294 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET | 14 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P68400 (Homo sapiens) Explore P68400 Go to UniProtKB: P68400 | |||||
PHAROS: P68400 GTEx: ENSG00000101266 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P68400 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UDP Query on UDP | E [auth A], I [auth C] | URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N |  | ||
| NAG Query on NAG | G [auth B], J [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| SO4 Query on SO4 | F [auth A], H [auth B], K [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.237
- R-Value Work: 0.217
- R-Value Observed: 0.218
- Space Group: I 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.35 | α = 90 |
| b = 137.19 | β = 103.05 |
| c = 153.07 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
| CBASS | data collection |
| iMOSFLM | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-09-14 Deposition Author(s): Janetzko, J., Lazarus, M.B., Walker, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM094263 |
Revision History (Full details and data files)
- Version 1.0: 2016-09-14
Type: Initial release - Version 1.1: 2016-10-26
Changes: Database references - Version 1.2: 2017-09-20
Changes: Author supporting evidence, Derived calculations - Version 1.3: 2019-12-25
Changes: Author supporting evidence - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
