SMTL ID : 2zr8.1

Crystal Structure of Modified Serine Racemase complexed with Serine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x PDD: N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE(Covalent)

PDD.1: 22 residues within 4Å: Chain A: F.56, K.57, S.81, S.82, G.83, N.84, H.85, P.151, Y.152, C.181, L.182, G.183, G.184, G.185, G.186, L.187, G.236, E.281, T.283, S.308, G.309 Ligands: SER.2 24 PLIP interactions: 22 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:K.57, A:P.151, A:E.281 Hydrogen bonds: A:S.82, A:G.83, A:N.84, A:N.84, A:H.85, A:G.183, A:G.183, A:G.184, A:G.185, A:G.186, A:L.187, A:S.308, S.2, S.2 Water bridges: A:K.57, A:K.112, A:P.151, A:L.188 Salt bridges: A:K.57, A:K.57 pi-Stacking: A:F.56 PDD.4: 22 residues within 4Å: Chain B: F.56, K.57, S.81, S.82, G.83, N.84, H.85, P.151, Y.152, C.181, L.182, G.183, G.184, G.185, G.186, L.187, G.236, E.281, T.283, S.308, G.309 Ligands: SER.5 24 PLIP interactions: 22 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:K.57, B:P.151, B:E.281 Hydrogen bonds: B:S.82, B:G.83, B:N.84, B:N.84, B:H.85, B:G.183, B:G.183, B:G.184, B:G.185, B:G.186, B:L.187, B:S.308, S.5, S.5 Water bridges: B:K.57, B:K.112, B:P.151, B:L.188 Salt bridges: B:K.57, B:K.57 pi-Stacking: B:F.56

2 x SER: SERINE(Non-covalent)

SER.2: 12 residues within 4Å: Chain A: S.81, S.82, R.128, R.133, P.151, Y.152, D.235, G.236, A.237, Q.238, T.239 Ligands: PDD.1 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.82, A:R.128, A:D.235, A:G.236, A:Q.238, S.2, S.2 Water bridges: A:Y.126 Salt bridges: A:R.133 SER.5: 12 residues within 4Å: Chain B: S.81, S.82, R.128, R.133, P.151, Y.152, D.235, G.236, A.237, Q.238, T.239 Ligands: PDD.4 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.82, B:R.128, B:D.235, B:G.236, B:Q.238, S.5, S.5 Salt bridges: B:R.133

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.208, G.212, D.214, A.237 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.208, A:G.212, A:D.214, H2O.1, H2O.1, H2O.3 MG.6: 4 residues within 4Å: Chain B: E.208, G.212, D.214, A.237 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.208, B:G.212, B:D.214, H2O.5, H2O.5, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, M. et al., Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe. J.Biol.Chem. (2009)

Release Date

2009-07-28

Peptides

Uncharacterized protein C320.14: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uncharacterized protein C320.14

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