Download MendeleyCrystal structure of metallo peptidase from Rhodobacter sphaeroides liganded with phosphinate mimic of dipeptide L-Ala-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.
3LY0
Crystal structure of metallo peptidase from Rhodobacter sphaeroides liganded with phosphinate mimic of dipeptide L-Ala-D-Ala
- PDB DOI: https://doi.org/10.2210/pdb3LY0/pdb
- Classification: HYDROLASE
- Organism(s): Cereibacter sphaeroides 2.4.1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-02-25 Released: 2010-03-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.192
- R-Value Work: 0.169
- R-Value Observed: 0.170
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 |
| Dipeptidase AC. Metallo peptidase. MEROPS family M19 | 364 | Cereibacter sphaeroides 2.4.1 | Mutation(s): 0 Gene Names: RHOS4_24130, RSP_0802 |  | |
UniProt | |||||
Find proteins for Q3IZQ3 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IZQ3 Go to UniProtKB: Q3IZQ3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q3IZQ3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| LY0 Query on LY0 | C [auth A], F [auth B] | (2R)-3-[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid C6 H14 N O4 P XXVGIEKADYFHOF-CRCLSJGQSA-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: 1.40 Å
- R-Value Free: 0.192
- R-Value Work: 0.169
- R-Value Observed: 0.170
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 46.649 | α = 83.65 |
| b = 50.325 | β = 73.64 |
| c = 81.436 | γ = 67.65 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| BALBES | phasing |
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2010-03-09 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: 2010-03-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary - Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description
