4WN2
Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex III)
- PDB DOI: https://doi.org/10.2210/pdb4WN2/pdb
- Classification: transferase/transferase inhibitor
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): No 
- Deposited: 2014-10-10 Released: 2015-09-30 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.239 
- R-Value Work: 0.195 
- R-Value Observed: 0.197 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Xyloside xylosyltransferase 1 | 306 | Mus musculus | Mutation(s): 0  Gene Names: Xxylt1 EC: 2.4.2 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q3U4G3 (Mus musculus) Explore Q3U4G3  Go to UniProtKB:  Q3U4G3 | |||||
IMPC:  MGI:2146443 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q3U4G3 | ||||
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 |
Coagulation factor IX | B [auth D] | 50 | Homo sapiens | Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740 | |||||
PHAROS:  P00740 GTEx:  ENSG00000101981  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00740 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
UDP Query on UDP | E [auth A] | URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N | |||
SO4 Query on SO4 | F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
MN Query on MN | D [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.239 
- R-Value Work: 0.195 
- R-Value Observed: 0.197 
- Space Group: P 3
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 89.509 | α = 90 |
b = 89.509 | β = 90 |
c = 43.053 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
Entry History 
Revision History (Full details and data files)
- Version 1.0: 2015-09-30
Type: Initial release - Version 1.1: 2016-04-20
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-12-27
Changes: Data collection, Database references, Structure summary