5CXY
Structure of a Glycosyltransferase in Complex with Inhibitor
- PDB DOI: https://doi.org/10.2210/pdb5CXY/pdb
- Classification: Transferase/Transferase Inhibitor
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2015-07-29 Released: 2016-09-07 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.235 
- R-Value Work: 0.198 
- R-Value Observed: 0.200 
This is version 2.1 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 |
Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase | 323 | Homo sapiens | Mutation(s): 0  Gene Names: ST8SIA3, SIAT8C EC: 2.4.99 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O43173 (Homo sapiens) Explore O43173  Go to UniProtKB:  O43173 | |||||
PHAROS:  O43173 GTEx:  ENSG00000177511  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O43173 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
55T Query on 55T | I [auth A], L [auth B] | 5'-O-[(R)-[(S)-[3-(acetylamino)phenyl](phosphono)methoxy](hydroxy)phosphoryl]cytidine C18 H24 N4 O12 P2 DIZKZDHPUBLUSO-NHMWIVBRSA-N | |||
NAG Query on NAG | J [auth B], K [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.235 
- R-Value Work: 0.198 
- R-Value Observed: 0.200 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 72.84 | α = 90 |
b = 96.64 | β = 90 |
c = 124.78 | γ = 90 |
Software Name | Purpose |
---|---|
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2016-09-07  Deposition Author(s): Volkers, G., Strynadka, N.C.J.
Revision History (Full details and data files)
- Version 1.0: 2016-09-07
Type: Initial release - Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary