Download MendeleyInhibitor design to Ribonuclease A: The binding of two 5'phosphate uridine analogues
Tsirkone, V.G., Dossi, K., Drakou, C., Zographos, S.E., Kontou, M., Leonidas, D.D.(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun
3DXH
Ribonuclease A uridine 5' diphosphate complex
- PDB DOI: https://doi.org/10.2210/pdb3DXH/pdb
- Classification: HYDROLASE
- Organism(s): Bos taurus
- Mutation(s): No
- Deposited: 2008-07-24 Released: 2009-06-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.225
- R-Value Work: 0.188
- R-Value Observed: 0.190
This is version 1.3 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 |
| Ribonuclease pancreatic | 124 | Bos taurus | Mutation(s): 0 EC: 3.1.27.5 |  | |
UniProt | |||||
Find proteins for P61823 (Bos taurus) Explore P61823 Go to UniProtKB: P61823 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61823 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UDP Query on UDP | C [auth A], D [auth A], E [auth B], F [auth B] | URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.225
- R-Value Work: 0.188
- R-Value Observed: 0.190
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 100.003 | α = 90 |
| b = 32.337 | β = 90.72 |
| c = 72.299 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MAR345 | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2009-06-16 Deposition Author(s): Tsirkone, V.G., Dossi, K., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G., Kontou, M.
Revision History (Full details and data files)
- Version 1.0: 2009-06-16
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
