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Schiebel, J., Heine, A., Klebe, G.To be published.
5DR3
Endothiapepsin in complex with fragment 333
- PDB DOI: https://doi.org/10.2210/pdb5DR3/pdb
- Classification: HYDROLASE
- Organism(s): Cryphonectria parasitica
- Mutation(s): No
- Deposited: 2015-09-15 Released: 2016-09-28
- Funding Organization(s): BMBF
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.24 ?
- R-Value Free: 0.133
- R-Value Work: 0.112
- R-Value Observed: 0.113
Starting Model: experimental
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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 | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 5GL Query on 5GL | I [auth A] | 4-propan-2-ylsulfanyl-1-propyl-6,7-dihydro-5~{H}-cyclopenta[d]pyrimidin-2-one C13 H20 N2 O S KUWKRQXLULNLGL-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | B [auth A], C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| DMS Query on DMS | G [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | E [auth A], F [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.24 ?
- R-Value Free: 0.133
- R-Value Work: 0.112
- R-Value Observed: 0.113
- Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 45.288 | α = 90 |
| b = 73.032 | β = 109.5 |
| c = 52.829 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PHASER | phasing |
| XDS | data reduction |
| XDS | data scaling |
| Coot | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-09-28 Deposition Author(s): Schiebel, J., Heine, A., Klebe, G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| BMBF | Germany | 05K13RM1 |
Revision History (Full details and data files)
- Version 1.0: 2016-09-28
Type: Initial release - Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-11-20
Changes: Structure summary
