Download MendeleyEnthalpic cost of water removal from a hydrophobic glucose binding cavity on HK620 tailspike protein.
Gohlke, U., Broeker, N.K., Kunstmann, S., Santer, M., Heinemann, U., Lipowski, R., Seckler, R., Barbirz, S.To be published.
4XMY
Tailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620 in complex with pentasaccharide
- PDB DOI: https://doi.org/10.2210/pdb4XMY/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Enterobacteria phage HK620
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2015-01-15 Released: 2016-01-27
- Funding Organization(s): German Research Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.174
- R-Value Work: 0.144
- R-Value Observed: 0.146
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 3.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tail spike protein | 599 | Enterobacteria phage HK620 | Mutation(s): 2 |  | |
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 | |||||
| |||||
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)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 6 | N/A | N/A | |
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TRS Query on TRS | C [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| FMT Query on FMT | D [auth A], E [auth A], F [auth A], G [auth A], H [auth A] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
| NA Query on NA | I [auth A], J [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.174
- R-Value Work: 0.144
- R-Value Observed: 0.146
- Space Group: P 3 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 74.234 | α = 90 |
| b = 74.234 | β = 90 |
| c = 174.578 | γ = 120 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| Aimless | data scaling |
| REFMAC | phasing |
| ARP | model building |
| Coot | model building |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-01-27 Deposition Author(s): Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| German Research Foundation | Germany | BA 4046/1-1 |
Revision History (Full details and data files)
- Version 1.0: 2016-01-27
Type: Initial release - Version 2.0: 2017-09-06
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
