Download MendeleyDiaminopimelate Decarboxylase uses a Versatile Active Site for Stereospecific Decarboxylation
Levdikov, V., Blagova, L., Bose, N., Momany, C.To be published.
1KO0
Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase
- PDB DOI: https://doi.org/10.2210/pdb1KO0/pdb
- Classification: LYASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2001-12-19 Released: 2003-11-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.246
- R-Value Work: 0.181
wwPDB Validation 3D Report Full Report
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 |
| Diaminopimelate decarboxylase | 425 | Escherichia coli | Mutation(s): 0 Gene Names: lysA EC: 4.1.1.20 |  | |
UniProt | |||||
Find proteins for P00861 (Escherichia coli (strain K12)) Explore P00861 Go to UniProtKB: P00861 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00861 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PLP Query on PLP | B [auth A] | PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N |  | ||
| LYS Query on LYS | C [auth A] | LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O |  | ||
| DLY Query on DLY | D [auth A] | D-LYSINE C6 H14 N2 O2 KDXKERNSBIXSRK-RXMQYKEDSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.246
- R-Value Work: 0.181
- Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.997 | α = 90 |
| b = 98.997 | β = 90 |
| c = 176.966 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CCP4 | model building |
| REFMAC | refinement |
| CCP4 | phasing |
Entry History
Deposition Data
- Released Date: 2003-11-11 Deposition Author(s): Levdikov, V., Blagova, L., Bose, N., Momany, C.
Revision History (Full details and data files)
- Version 1.0: 2003-11-11
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description
