SMTL ID : 5x2l.1

Crystal Structure of Human Serine Racemase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 16 residues within 4Å: Chain A: F.55, K.56, N.86, N.154, V.184, G.185, G.186, G.187, G.188, M.189, G.239, V.240, E.283, T.285, S.313, G.314 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.55, A:K.56 Hydrogen bonds: A:N.86, A:N.154, A:G.185, A:G.186, A:G.187, A:G.188, A:M.189, A:S.313 Water bridges: A:N.86, A:L.190 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.3: 15 residues within 4Å: Chain B: F.55, K.56, N.86, V.184, G.185, G.186, G.187, G.188, M.189, G.239, V.240, E.283, T.285, S.313, G.314 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.55, B:K.56 Hydrogen bonds: B:N.86, B:N.154, B:G.185, B:G.186, B:G.187, B:G.188, B:M.189, B:S.313 Water bridges: B:N.86, B:P.153, B:P.183, B:L.190 Salt bridges: B:K.56 pi-Stacking: B:F.55

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.210, A.214, D.216, S.242 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.210, A:A.214, A:D.216, H2O.2, H2O.2, H2O.2 MG.4: 4 residues within 4Å: Chain B: E.210, A.214, D.216, V.240 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.210, B:A.214, B:D.216, H2O.8, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takahara, S. et al., Design, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase. Bioorg. Med. Chem. Lett. (2017)

Release Date

2018-01-31

Peptides

Serine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine racemase