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Radeva, N., Heine, A., Klebe, G.To be published.
4Y56
Endothiapepsin in complex with fragment 58
- PDB DOI: https://doi.org/10.2210/pdb4Y56/pdb
- Classification: HYDROLASE
- Organism(s): Cryphonectria parasitica
- Mutation(s): No
- Deposited: 2015-02-11 Released: 2016-03-02
- Funding Organization(s): BMBF
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.63 Å
- R-Value Free: 0.171
- R-Value Work: 0.142
- R-Value Observed: 0.144
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Endothiapepsin | 330 | Cryphonectria parasitica | Mutation(s): 0 EC: 3.4.23.22 |  | |
UniProt | |||||
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838 Go to UniProtKB: P11838 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P11838 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 47J Query on 47J | G [auth A] | 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine C6 H11 N3 DAOWQCXPMWGSBW-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | B [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| DMS Query on DMS | C [auth A], D [auth A], E [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | F [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.63 Å
- R-Value Free: 0.171
- R-Value Work: 0.142
- R-Value Observed: 0.144
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 45.174 | α = 90 |
| b = 72.773 | β = 109.67 |
| c = 52.528 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Coot | model building |
| XDS | data reduction |
| PHASER | phasing |
| XDS | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-03-02 Deposition Author(s): Radeva, N., Heine, A., Klebe, G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| BMBF | Germany | 05K13RM1 |
Revision History (Full details and data files)
- Version 1.0: 2016-03-02
Type: Initial release - Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description - Version 1.2: 2024-11-13
Changes: Structure summary
