Download MendeleyCrystal structure of diaminopimelate decarboxylase from Helicobacter pylori
Hu, T., Wu, D., Ding, J., Jiang, H., Shen, X.To be published.
3C5Q | pdb_00003c5q
3C5Q | pdb_00003c5q
Crystal structure of diaminopimelate decarboxylase (I148L mutant) from Helicobacter pylori complexed with L-lysine
- PDB DOI: https://doi.org/10.2210/pdb3C5Q/pdb
- Classification: LYASE
- Organism(s): Helicobacter pylori
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-02-01 Released: 2008-05-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.253 (Depositor), 0.205 (DCC)
- R-Value Work: 0.202 (Depositor), 0.204 (DCC)
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Diaminopimelate decarboxylase | 425 | Helicobacter pylori | Mutation(s): 0 Gene Names: lysA EC: 4.1.1.20 |  | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B4XMC6 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PLP Download:Ideal Coordinates CCD File | B [auth A] | PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N |  | ||
| LYS Download:Ideal Coordinates CCD File | C [auth A] | LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O |  | ||
| GOL Download:Ideal Coordinates CCD File | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.253 (Depositor), 0.205 (DCC)
- R-Value Work: 0.202 (Depositor), 0.204 (DCC)
Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 79.111 | α = 90 |
| b = 79.111 | β = 90 |
| c = 134.821 | γ = 120 |
| Software Name | Purpose |
|---|---|
| d*TREK | data processing |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| CrystalClear | data collection |
| d*TREK | data reduction |
| d*TREK | data scaling |
| CNS | phasing |
Entry History
Revision History (Full details and data files)
- Version 1.0: 2008-05-27
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations
