Download MendeleyCrystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K
Iizuka, Y., Kikuchi, M., Yamauchi, T., Tsunoda, M.To be published.
9JD2
Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K
- PDB DOI: https://doi.org/10.2210/pdb9JD2/pdb
- Classification: TRANSFERASE
- Organism(s): Aeropyrum pernix K1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-08-30 Released: 2024-09-18
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.62 Å
- R-Value Free: 0.168
- R-Value Work: 0.123
Starting Model: experimental
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This is version 1.0 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 |
| S-methyl-5'-thioadenosine phosphorylase | 275 | Aeropyrum pernix K1 | Mutation(s): 0 Gene Names: mtnP, APE_1885 EC: 2.4.2.28 |  | |
UniProt | |||||
Find proteins for Q9YAQ8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YAQ8 Go to UniProtKB: Q9YAQ8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9YAQ8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MTA (Subject of Investigation/LOI) Query on MTA | C [auth A] | 5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N |  | ||
| PO4 (Subject of Investigation/LOI) Query on PO4 | B [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.62 Å
- R-Value Free: 0.168
- R-Value Work: 0.123
- Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 79.048 | α = 90 |
| b = 79.048 | β = 90 |
| c = 233.48 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| Coot | model building |
| MOLREP | phasing |
| Aimless | data scaling |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-09-18 Deposition Author(s): Iizuka, Y., Kikuchi, M., Yamauchi, T., Tsunoda, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-09-18
Type: Initial release
