Download MendeleyCationic trypsin in complex with a derivative of benzamidine
Sandner, A., Heine, A., Klebe, G.To be published.
6ZQ2
Cationic trypsin in complex with a derivative of benzamidine
- PDB DOI: https://doi.org/10.2210/pdb6ZQ2/pdb
- Classification: HYDROLASE
- Organism(s): Bos taurus
- Mutation(s): No
- Deposited: 2020-07-09 Released: 2021-07-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.29 Å
- R-Value Free: 0.145
- R-Value Work: 0.127
- R-Value Observed: 0.128
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 |
| Cationic trypsin | 223 | Bos taurus | Mutation(s): 0 EC: 3.4.21.4 |  | |
UniProt | |||||
Find proteins for P00760 (Bos taurus) Explore P00760 Go to UniProtKB: P00760 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00760 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 32U Query on 32U | B [auth A] | D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide C22 H28 N5 O2 VZFTWWJAUZOJDH-MOPGFXCFSA-O |  | ||
| SO4 Query on SO4 | E [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth A], F [auth A], G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000600 (32U) Query on PRD_000600 | B [auth A] | D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide | Peptide-like / Thrombin inhibitor | | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.29 Å
- R-Value Free: 0.145
- R-Value Work: 0.127
- R-Value Observed: 0.128
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.803 | α = 90 |
| b = 54.803 | β = 90 |
| c = 108.558 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2021-07-21 Deposition Author(s): Sandner, A., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2021-07-21
Type: Initial release - Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description - Version 1.2: 2024-11-20
Changes: Structure summary
