Download MendeleyStructure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate
Bitto, E., Bingman, C.A., Grobosky, C.L.To be published.
4KX3
Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate
- PDB DOI: https://doi.org/10.2210/pdb4KX3/pdb
- Classification: HYDROLASE
- Organism(s): Mus musculus
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2013-05-24 Released: 2013-06-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 ?
- R-Value Free: 0.216 (Depositor), 0.225 (DCC)
- R-Value Work: 0.153 (Depositor), 0.167 (DCC)
- R-Value Observed: 0.156 (Depositor)
Starting Model: experimental
View more details
This is version 2.0 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 |
| Isoform 1 of Cytosolic 5'-nucleotidase 3A | 297 | Mus musculus | Mutation(s): 2 Gene Names: Nt5c3a, Nt5c3 EC: 3.1.3.5 (PDB Primary Data), 3.1.3.91 (PDB Primary Data) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9D020 (Mus musculus) Explore Q9D020 Go to UniProtKB: Q9D020 | |||||
IMPC: MGI:1927186 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9D020 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TMP Query on TMP | B [auth A] | THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N |  | ||
| EPE Query on EPE | G [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | D [auth A], E [auth A], F [auth A], H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MG Query on MG | C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CME Query on CME | A | L-PEPTIDE LINKING | C5 H11 N O3 S2 |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 ?
- R-Value Free: 0.216 (Depositor), 0.225 (DCC)
- R-Value Work: 0.153 (Depositor), 0.167 (DCC)
- R-Value Observed: 0.156 (Depositor)
Space Group: P 43 2 2
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 46.872 | ¦Á = 90 |
| b = 46.872 | ¦Â = 90 |
| c = 285.873 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data collection |
Entry History
Deposition Data
- Released Date: 2013-06-05 Deposition Author(s): Bitto, E., Bingman, C.A., Grobosky, C.L.
Revision History (Full details and data files)
- Version 1.0: 2013-06-05
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 2.0: 2025-02-12
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
