SMTL ID : 4riz.1 (1 other biounit)

The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Covalent)

PMP.1: 15 residues within 4Å: Chain A: M.94, G.153, G.154, S.155, N.158, H.193, S.195, G.248, T.250, D.275, A.277, N.304, Q.306, K.307 Chain B: T.354 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:T.354, A:G.154, A:S.155, A:S.155, A:N.158, A:N.304, A:Q.306 Water bridges: B:G.353 Hydrophobic interactions: A:H.193, A:A.277 pi-Stacking: A:H.193

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: T.314, H.356 Chain B: T.314, H.356 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.314 Water bridges: A:S.152, A:T.314, A:T.314, B:T.314, B:T.314, B:H.356 NA.6: 8 residues within 4Å: Chain A: E.174, P.175 Chain B: R.183, L.205, G.206, T.207, A.208, A.209 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.183, B:G.206, B:A.208, B:A.209

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain B: L.139, F.140, R.289, L.292, A.293, I.295, E.296 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.139, B:L.292 GOL.4: 1 residues within 4Å: Chain B: A.263 No protein-ligand interaction detected (PLIP) GOL.5: 9 residues within 4Å: Chain B: Y.310, L.377, D.380, G.381, L.384, L.457, L.458, N.459, P.460 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.310, B:L.377, B:N.459 Water bridges: B:N.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., The crystal structure of y333q mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745. To be Published

Release Date

2014-11-12

Peptides

Pyridoxal-dependent decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal-dependent decarboxylase

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