2X6Y
Tailspike protein mutant D339A of E.coli bacteriophage HK620 in complex with hexasaccharide
- PDB DOI: https://doi.org/10.2210/pdb2X6Y/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Enterobacteria phage HK620
- Expression System: Escherichia coli BL21
- Mutation(s): Yes 
- Deposited: 2010-02-22 Released: 2011-03-02 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.171 
- R-Value Work: 0.132 
- R-Value Observed: 0.134 
wwPDB Validation   3D Report Full Report
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 |
TAIL SPIKE PROTEIN | 600 | Enterobacteria phage HK620 | Mutation(s): 1  | ||
UniProt | |||||
Find proteins for Q9AYY6 (Enterobacteria phage HK620) Explore Q9AYY6  Go to UniProtKB:  Q9AYY6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9AYY6 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | B | 6 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G22623XU GlyCosmos:  G22623XU |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
TRS Query on TRS | E [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
NA Query on NA | C [auth A], D [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.171 
- R-Value Work: 0.132 
- R-Value Observed: 0.134 
- Space Group: P 3 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 74.336 | α = 90 |
b = 74.336 | β = 90 |
c = 174.977 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2011-03-02  Deposition Author(s): Lorenzen, N.K., Mueller, J.J., Heinemann, U., Seckler, R., Barbirz, S.
Revision History (Full details and data files)
- Version 1.0: 2011-03-02
Type: Initial release - Version 1.1: 2014-02-05
Changes: Database references, Version format compliance - Version 1.2: 2019-01-30
Changes: Data collection, Experimental preparation, Other - Version 1.3: 2019-02-06
Changes: Data collection, Experimental preparation - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary