4KWN
A new stabilizing water structure at the substrate binding site in ribosome inactivating protein from Momordica balsamina at 1.80 A resolution
- PDB DOI: https://doi.org/10.2210/pdb4KWN/pdb
- Classification: HYDROLASE
- Organism(s): Momordica balsamina
- Mutation(s): No 
- Deposited: 2013-05-24 Released: 2013-06-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.214 
- R-Value Work: 0.178 
- R-Value Observed: 0.180 
This is version 1.3 of the entry. See complete history. 
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 | ||||
Sequence AnnotationsExpand | |||||
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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 | |||
GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.214 
- R-Value Work: 0.178 
- R-Value Observed: 0.180 
- Space Group: H 3
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 130.212 | α = 90 |
b = 130.212 | β = 90 |
c = 39.847 | 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: 2013-06-12  Deposition Author(s): Yamini, S., Pandey, S., Singh, A., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2013-06-12
Type: Initial release - Version 1.1: 2013-07-17
Changes: Structure summary - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary