Download MendeleyThe Yersinia YopO - actin complex with MgADP
Lee, W.L., Grimes, J.M., Robinson, R.C.To be published.
5CE3 | pdb_00005ce3
The Yersinia YopO - actin complex with MgADP
- PDB DOI: https://doi.org/10.2210/pdb5CE3/pdb
- Classification: CONTRACTILE PROTEIN/TRANSFERASE
- Organism(s): Spodoptera frugiperda, Yersinia enterocolitica
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2015-07-06 Released: 2016-07-06
- Funding Organization(s): Agency for Science, Technology and Research (A*STAR), Wellcome Trust
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.93 Å
- R-Value Free: 0.240 (Depositor), 0.240 (DCC)
- R-Value Work: 0.196 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.198 (Depositor)
Starting Model: experimental
View more details
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Actin | 376 | Spodoptera frugiperda | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for G3CKA6 (Spodoptera frugiperda) Explore G3CKA6 Go to UniProtKB: G3CKA6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | G3CKA6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protein kinase YopO | 643 | Yersinia enterocolitica | Mutation(s): 5 Gene Names: yopO |  | |
UniProt | |||||
Find proteins for Q93KQ6 (Yersinia enterocolitica) Explore Q93KQ6 Go to UniProtKB: Q93KQ6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q93KQ6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | E [auth A], I [auth C] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| ADP Query on ADP | G [auth B], K [auth D] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
| CA Query on CA | F [auth A], J [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| MG Query on MG | H [auth B], L [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.93 Å
- R-Value Free: 0.240 (Depositor), 0.240 (DCC)
- R-Value Work: 0.196 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.198 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 108.73 | α = 90 |
| b = 121.75 | β = 104.88 |
| c = 118.58 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-07-06 Deposition Author(s): Lee, W.L., Singaravelu, P., Grimes, J.M., Robinson, R.C.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Agency for Science, Technology and Research (A*STAR) | Singapore | -- |
| Wellcome Trust | United Kingdom | 090532/Z/09/Z |
Revision History (Full details and data files)
- Version 1.0: 2016-07-06
Type: Initial release - Version 1.1: 2020-02-05
Changes: Data collection, Derived calculations - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
