4ZT8
Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a pyrimidine base, cytosine at 1.98 A resolution
- PDB DOI: https://doi.org/10.2210/pdb4ZT8/pdb
- Entry: 4ZT8 supersedes: 4KJH
- Classification: HYDROLASE
- Organism(s): Momordica balsamina
- Mutation(s): No
- Deposited: 2015-05-14 Released: 2015-06-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.204
- R-Value Work: 0.178
- R-Value Observed: 0.180
This is version 1.5 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 |
| Ribosome inactivating protein | 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 3 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 |  | ||
| CYT Query on CYT | E [auth A] | 6-AMINOPYRIMIDIN-2(1H)-ONE C4 H5 N3 O OPTASPLRGRRNAP-UHFFFAOYSA-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: 1.98 Å
- R-Value Free: 0.204
- R-Value Work: 0.178
- R-Value Observed: 0.180
- Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 130.258 | α = 90 |
| b = 130.258 | β = 90 |
| c = 39.939 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2015-06-03 Deposition Author(s): Yamini, S., Pandey, S., Kaur, P., Sharma, S., Singh, T.P.
- This entry supersedes: 4KJH
Revision History (Full details and data files)
- Version 1.0: 2015-06-03
Type: Initial release - Version 1.1: 2015-08-05
Changes: Other - Version 1.2: 2016-07-27
Changes: Database references - Version 1.3: 2020-01-01
Changes: Database references, Derived calculations - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
