Download MendeleyLegionella pneumophila DHDPS: The First Case of Non-Lysine Inhibition in a Gram-Negative Pathogen
Siddiqui, T., Paxman, J.J., Dogovski, C., Panjikar, S., Perugini, M.A.To be published.
4NQ1
Legionella pneumophila dihydrodipicolinate synthase with first substrate pyruvate bound in the active site
- PDB DOI: https://doi.org/10.2210/pdb4NQ1/pdb
- Classification: LYASE
- Organism(s): Legionella pneumophila 2300/99 Alcoy
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-11-23 Released: 2014-01-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.187
- R-Value Work: 0.147
- R-Value Observed: 0.148
wwPDB Validation 3D Report Full Report
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 |
| 4-hydroxy-tetrahydrodipicolinate synthase | 290 | Legionella pneumophila 2300/99 Alcoy | Mutation(s): 0 Gene Names: dapA, lpa_03319 EC: 4.2.1.52 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | I [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| MRD Query on MRD | C [auth A] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N |  | ||
| CL Query on CL | D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | G [auth A], H [auth A], M [auth B], N [auth B], O [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| KPI Query on KPI | A, B | L-PEPTIDE LINKING | C9 H16 N2 O4 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.187
- R-Value Work: 0.147
- R-Value Observed: 0.148
- Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 89.31 | α = 90 |
| b = 89.31 | β = 90 |
| c = 290.18 | γ = 120 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2014-01-01 Deposition Author(s): Siddiqui, T., Paxman, J.J.
Revision History (Full details and data files)
- Version 1.0: 2014-01-01
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2023-11-29
Changes: Data collection
