SMTL ID : 4rlg.2 (1 other biounit)

The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PMP.1: 16 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: T.354 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.246 Hydrogen bonds: A:G.154, A:S.155, A:S.155, A:N.158, A:T.250, A:T.250, A:N.304, A:Q.306, B:T.354 pi-Stacking: A:H.193 Water bridges: B:G.353 PMP.6: 17 residues within 4Å: Chain A: G.353, T.354 Chain B: 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 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.246 Hydrogen bonds: B:G.154, B:S.155, B:N.158, B:T.250, B:N.304, B:Q.306, A:G.353, A:T.354 pi-Stacking: B:H.193

2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.2: 9 residues within 4Å: Chain A: S.189, E.190, A.191, A.192, H.193, T.194, Q.197, V.210 Ligands: ABU.3 No protein-ligand interaction detected (PLIP) ABU.3: 7 residues within 4Å: Chain A: A.192, H.193, T.194, L.196, Q.197, V.210 Ligands: ABU.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.194 Hydrogen bonds: A:Q.197, A:Q.197, B:Y.336

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.387, E.390, Q.394, D.468, F.471, K.472 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.468, A:D.468, A:K.472 GOL.7: 5 residues within 4Å: Chain B: R.387, G.391, I.467, D.468, F.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.391, B:D.468, B:D.468 Water bridges: B:R.395

2 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: V.392, R.393, R.395, L.398 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.392, A:L.398 K.8: 4 residues within 4Å: Chain B: V.392, R.393, R.395, L.398 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.392, B:R.395, B:L.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745. TO BE PUBLISHED

Release Date

2014-10-29

Peptides

Pyridoxal-dependent decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

Pyridoxal-dependent decarboxylase

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