Download MendeleyCrystal Structure of the Nicotiana glutinosa Ribonuclease NT in Complex with Nucleotide Monophosphates
Kawano, S., Kakuta, Y., Kimura, M.To be published.
1VD3
Ribonuclease NT in complex with 2'-UMP
- PDB DOI: https://doi.org/10.2210/pdb1VD3/pdb
- Classification: HYDROLASE
- Organism(s): Nicotiana glutinosa
- Expression System: Komagataella pastoris
- Mutation(s): No
- Deposited: 2004-03-18 Released: 2005-04-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 ?
- R-Value Free: 0.251
- R-Value Work: 0.209
- R-Value Observed: 0.209
Starting Model: experimental
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This is version 1.4 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 |
| RNase NGR3 | 217 | Nicotiana glutinosa | Mutation(s): 0 EC: 3.1.27.1 |  | |
UniProt | |||||
Find proteins for Q9SSV1 (Nicotiana glutinosa) Explore Q9SSV1 Go to UniProtKB: Q9SSV1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SSV1 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| U2P Query on U2P | B [auth A] | PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL]
ESTER C9 H13 N2 O9 P HQIDPEYTETUCNF-XVFCMESISA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 ?
- R-Value Free: 0.251
- R-Value Work: 0.209
- R-Value Observed: 0.209
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 37.232 | ¦Á = 90 |
| b = 68.984 | ¦Â = 90 |
| c = 73.863 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2005-04-26 Deposition Author(s): Kawano, S., Kakuta, Y., Kimura, M.
Revision History (Full details and data files)
- Version 1.0: 2005-04-26
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.4: 2024-10-30
Changes: Structure summary
