SMTL ID : 4rm1.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

PMP.1: 17 residues within 4Å: Chain A: M.94, G.153, G.154, S.155, N.158, H.193, S.195, T.246, G.248, T.250, D.275, A.277, N.304, Q.306, K.307 Chain B: G.353, T.354 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.246, A:A.277 Hydrogen bonds: A:G.154, A:S.155, A:N.158, A:H.193, A:N.304, A:Q.306, B:G.353, B:T.354 Salt bridges: A:H.193 pi-Stacking: A:H.193 Water bridges: B:T.354

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: L.139, F.140, G.141, R.289, L.292, A.293, I.295, E.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.140, A:E.296 Water bridges: A:R.289 GOL.3: 4 residues within 4Å: Chain A: L.119, E.120, R.127, A.339 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127, A:R.127 GOL.4: 5 residues within 4Å: Chain A: A.191, A.192, H.193, T.194, T.250 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.191, A:T.194, A:T.194 Water bridges: A:T.194, A:T.250, A:T.251 GOL.6: 6 residues within 4Å: Chain B: R.412, A.420, D.424, R.448, G.449, G.450 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.412, B:D.424, B:R.448 Water bridges: B:G.450, B:R.451 GOL.7: 7 residues within 4Å: Chain B: L.139, F.140, R.289, W.290, L.292, A.293, I.295 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.140 Water bridges: B:E.296 GOL.8: 4 residues within 4Å: Chain B: S.189, E.190, V.210, P.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.189, B:Q.197 Water bridges: B:V.210

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: T.314, H.356 Chain B: T.314, H.356 Ligand excluded by PLIP

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
B

B
A

Pyridoxal-dependent decarboxylase

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