Download MendeleyCrystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN and phosphonate mimic of dipeptide L-Leu-D-Ala
Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., Sauder, J.M., Burley, S.K., Almo, S.C.To be published.
3NEH
Crystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN and phosphonate mimic of dipeptide L-Leu-D-Ala
- PDB DOI: https://doi.org/10.2210/pdb3NEH/pdb
- Classification: LYASE
- Organism(s): Listeria monocytogenes serotype 4b str. F2365
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-06-08 Released: 2010-06-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.64 Å
- R-Value Free: 0.219
- R-Value Work: 0.197
- R-Value Observed: 0.198
This is version 1.3 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 |
| Renal dipeptidase family protein | 318 | Listeria monocytogenes serotype 4b str. F2365 | Mutation(s): 0 Gene Names: LMOf2365_2435 EC: 4.99.1.1 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| L3A Query on L3A | C [auth A], F [auth B] | (2R)-3-[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]-2-methylpropanoic acid C9 H20 N O4 P PYHFMEIRRPJIRC-JGVFFNPUSA-N |  | ||
| ZN Query on ZN | D [auth A], E [auth A], G [auth B], H [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.64 Å
- R-Value Free: 0.219
- R-Value Work: 0.197
- R-Value Observed: 0.198
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.834 | α = 90 |
| b = 79.453 | β = 90 |
| c = 152.014 | γ = 90 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| BALBES | phasing |
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2010-06-30 Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2010-06-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2021-02-10
Changes: Advisory, Database references, Derived calculations, Structure summary - Version 1.3: 2023-09-06
Changes: Advisory, Data collection, Database references, Refinement description
