Download MendeleyCrystal Structure of the Prolidase from Pyrococcus horikoshii OT3
Mizutani, H., Kunishima, N.To be published.
1WY2 | pdb_00001wy2
Crystal Structure of the Prolidase from Pyrococcus horikoshii OT3
- PDB DOI: https://doi.org/10.2210/pdb1WY2/pdb
- Classification: HYDROLASE
- Organism(s): Pyrococcus horikoshii OT3
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2005-02-04 Released: 2005-02-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.210 (Depositor), 0.180 (DCC)
- R-Value Work: 0.187 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.187 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Xaa-Pro dipeptidase | 351 | Pyrococcus horikoshii OT3 | Mutation(s): 0 EC: 3.4.13.9 |  | |
UniProt | |||||
Find proteins for O58885 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58885 Go to UniProtKB: O58885 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O58885 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CAC Query on CAC | C [auth A], I [auth B] | CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M |  | ||
| GOL Query on GOL | G [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | D [auth A], E [auth A], J [auth B], K [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.210 (Depositor), 0.180 (DCC)
- R-Value Work: 0.187 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.187 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.697 | α = 90 |
| b = 105.876 | β = 90 |
| c = 106.291 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2005-02-22 Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2005-02-22
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
