Download MendeleyCrystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Legionella pneumophila in complex with NAD
DeBouver, N.D., Mayclin, S.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.To be published.
6XMY
Crystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Legionella pneumophila in complex with NAD
- PDB DOI: https://doi.org/10.2210/pdb6XMY/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-07-01 Released: 2020-07-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.172
- R-Value Work: 0.138
- R-Value Observed: 0.139
This is version 1.1 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 |
| 4-hydroxythreonine-4-phosphate dehydrogenase | 332 | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | Mutation(s): 0 Gene Names: pdxA, lpg0299 EC: 1.1.1.262 |  | |
UniProt | |||||
Find proteins for Q3V872 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q3V872 Go to UniProtKB: Q3V872 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q3V872 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAD (Subject of Investigation/LOI) Query on NAD | B [auth A] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N |  | ||
| SO4 Query on SO4 | C [auth A], J [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| PO4 Query on PO4 | D [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| ZN Query on ZN | K [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], F [auth A], G [auth A], H [auth A], I [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.172
- R-Value Work: 0.138
- R-Value Observed: 0.139
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 153.35 | α = 90 |
| b = 36.77 | β = 103.07 |
| c = 56.62 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MoRDa | phasing |
Entry History
Deposition Data
- Released Date: 2020-07-22 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2020-07-22
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Database references, Derived calculations, Refinement description
