Download MendeleyCrystal structure of a dihydrolipoyl dehydrogenase from Neisseria gonorrhoeae bound to FAD
Edwards, T.E., Horanyi, P.S., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)To be published.
5U25
Crystal structure of a dihydrolipoyl dehydrogenase from Neisseria gonorrhoeae bound to FAD
- PDB DOI: https://doi.org/10.2210/pdb5U25/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Neisseria gonorrhoeae
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-11-29 Released: 2016-12-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.209
- R-Value Work: 0.169
- R-Value Observed: 0.171
This is version 1.2 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 |
| Dihydrolipoamide dehydrogenase (E3 component of pyruvate and 2-oxoglutarate dehydrogenase complexes) | 602 | Neisseria gonorrhoeae | Mutation(s): 0 Gene Names: lpdA, WHOF_00599C, WHOF_01471, WHOG_01174, WHOG_01559, WHON_01176, WHON_01441, WHOO_01105, WHOO_01298, WHOW_00549... EC: 1.8.1.4 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FAD Query on FAD | B [auth A] | FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N |  | ||
| SO4 Query on SO4 | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| EDO Query on EDO | I [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.209
- R-Value Work: 0.169
- R-Value Observed: 0.171
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 142.66 | α = 90 |
| b = 142.66 | β = 90 |
| c = 70.39 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| MOLREP | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2016-12-21 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2016-12-21
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
