Download MendeleyCrystal structure of the complex of ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4(1H,3H)-dione at 2.57 A resolution
Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.To be published.
4KPV
Crystal structure of the complex of ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4(1H,3H)-dione at 2.57 A resolution
- PDB DOI: https://doi.org/10.2210/pdb4KPV/pdb
- Classification: HYDROLASE
- Organism(s): Momordica balsamina
- Mutation(s): No
- Deposited: 2013-05-14 Released: 2013-05-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.57 Å
- R-Value Free: 0.268
- R-Value Work: 0.244
- R-Value Observed: 0.245
Starting Model: experimental
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This is version 1.3 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 |
| rRNA N-glycosidase | 246 | Momordica balsamina | Mutation(s): 0 EC: 3.2.2.22 |  | |
UniProt | |||||
Find proteins for D9J2T9 (Momordica balsamina) Explore D9J2T9 Go to UniProtKB: D9J2T9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D9J2T9 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | B [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| URA Query on URA | C [auth A] | URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.57 Å
- R-Value Free: 0.268
- R-Value Work: 0.244
- R-Value Observed: 0.245
- Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 129.95 | α = 90 |
| b = 129.95 | β = 90 |
| c = 39.434 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2013-05-29 Deposition Author(s): Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2013-05-29
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary - Version 1.3: 2024-11-13
Changes: Structure summary
