SMTL ID : 3l6b.1

X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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, P.183, V.184, G.185, G.186, G.187, G.188, M.189, V.240, E.283, T.285, S.313, G.314 Ligands: MLI.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.55, A:K.56, A:V.240 Hydrogen bonds: A:K.56, A:N.86, A:G.185, A:G.186, A:G.187, A:G.188, A:M.189, A:S.313 Water bridges: A:N.154, A:L.190 Salt bridges: A:K.56 pi-Stacking: A:F.55 PLP.4: 16 residues within 4Å: Chain B: F.55, K.56, N.86, P.183, V.184, G.185, G.186, G.187, G.188, M.189, V.240, E.283, T.285, S.313, G.314 Ligands: MLI.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.55, B:K.56, B:V.240 Hydrogen bonds: B:K.56, B:N.86, B:G.185, B:G.186, B:G.187, B:G.188, B:M.189, B:S.313 Water bridges: B:N.154, B:L.190 Salt bridges: B:K.56 pi-Stacking: B:F.55

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: E.210, A.214, D.216 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.210, A:A.214, A:D.216, H2O.1, H2O.2, H2O.2 MN.5: 3 residues within 4Å: Chain B: E.210, A.214, D.216 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.210, B:A.214, B:D.216, H2O.9, H2O.10, H2O.10

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 11 residues within 4Å: Chain A: K.56, S.83, S.84, G.85, N.86, H.87, R.135, N.154, G.239, S.242 Ligands: PLP.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.84, A:S.84, A:G.85, A:N.86, A:H.87, A:R.135, A:N.154, A:S.242 Water bridges: A:G.186, A:K.241, A:S.242 Salt bridges: A:K.56, A:K.56, A:R.135 MLI.6: 11 residues within 4Å: Chain B: K.56, S.83, S.84, G.85, N.86, H.87, R.135, N.154, G.239, S.242 Ligands: PLP.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.84, B:S.84, B:G.85, B:N.86, B:H.87, B:R.135, B:N.154, B:S.242 Water bridges: B:G.186, B:K.241, B:S.242 Salt bridges: B:K.56, B:K.56, B:R.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, M.A. et al., The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding. J.Biol.Chem. (2010)

Release Date

2010-01-26

Peptides

Serine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine racemase

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