Download MendeleyTriglycine-Based Approach for Identifying the Substrate Recognition Site of an Enzyme
Nam, K.H.(2019) Crystals (Basel) 9
6KKF
Crystal structure of proteinase K complexed with a triglycine
- PDB DOI: https://doi.org/10.2210/pdb6KKF/pdb
- Classification: HYDROLASE
- Organism(s): Parengyodontium album
- Mutation(s): No
- Deposited: 2019-07-25 Released: 2019-09-25
- Funding Organization(s): National Research Foundation (Korea)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 ?
- R-Value Free: 0.218
- R-Value Work: 0.182
- R-Value Observed: 0.184
Starting Model: experimental
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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 |
| Proteinase K | 279 | Parengyodontium album | Mutation(s): 0 EC: 3.4.21.64 |  | |
UniProt | |||||
Find proteins for P06873 (Parengyodontium album) Explore P06873 Go to UniProtKB: P06873 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06873 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GGG (Subject of Investigation/LOI) Query on GGG | D [auth A] | glycylglycylglycine C6 H11 N3 O4 XKUKSGPZAADMRA-UHFFFAOYSA-N |  | ||
| CA Query on CA | B [auth A], C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 ?
- R-Value Free: 0.218
- R-Value Work: 0.182
- R-Value Observed: 0.184
- Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 38.512 | ¦Á = 90 |
| b = 67.685 | ¦Â = 111.393 |
| c = 43.592 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data scaling |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-09-25 Deposition Author(s): Nam, K.H.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Research Foundation (Korea) | Korea, Republic Of | 2017R1D1A1B03033087 |
| National Research Foundation (Korea) | Korea, Republic Of | 2017M3A9F6029736 |
Revision History (Full details and data files)
- Version 1.0: 2019-09-25
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-10-23
Changes: Structure summary
