The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Pyridoxal-dependent decarboxylase | A [auth B], B [auth A] | 486 | Sphaerobacter thermophilus DSM 20745 | Mutation(s): 0  Gene Names: Sthe_2364 EC: 4.1.1.15 | |
UniProt | |||||
Find proteins for D1C7D8 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C7D8  Go to UniProtKB:  D1C7D8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | D1C7D8 | ||||
Sequence AnnotationsExpand | |||||
|
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
TRS Query on TRS | J [auth B], K [auth B], S [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
GOL Query on GOL | E [auth B] F [auth B] G [auth B] H [auth B] I [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CL Query on CL | C [auth B], D [auth B], L [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Modified Residues 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
LLP Query on LLP | A [auth B], B [auth A] | L-PEPTIDE LINKING | C14 H22 N3 O7 P | LYS | |
MSE Query on MSE | A [auth B], B [auth A] | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 77.483 | α = 90 |
b = 118.566 | β = 90 |
c = 126.018 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-3000 | data collection |
MLPHARE | phasing |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |