SMTL ID : 1wtc.2 (1 other biounit)

Crystal Structure of S.pombe Serine Racemase complex with AMPPCP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: E.208, G.212, D.214 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.208, A:G.212, A:D.214, H2O.4, H2O.5, H2O.5 MG.2: 1 residues within 4Å: Ligands: ACP.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.208, G.212, D.214 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.208, B:G.212, B:D.214, H2O.14, H2O.15, H2O.15 MG.6: 1 residues within 4Å: Ligands: ACP.8 No protein-ligand interaction detected (PLIP)

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

PLP.3: 16 residues within 4Å: Chain A: F.56, K.57, N.84, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.56, A:K.57, A:E.281 Hydrogen bonds: A:N.84, A:G.183, A:G.184, A:G.185, A:G.186, A:L.187, A:S.308 Water bridges: A:N.84, A:L.188 Salt bridges: A:K.57 pi-Stacking: A:F.56 PLP.7: 16 residues within 4Å: Chain B: F.56, K.57, N.84, 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.56, B:K.57, B:E.281 Hydrogen bonds: B:N.84, B:G.183, B:G.184, B:G.185, B:G.186, B:L.187, B:S.308 Water bridges: B:N.84, B:L.188 Salt bridges: B:K.57 pi-Stacking: B:F.56

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.4: 17 residues within 4Å: Chain A: N.25, K.52, M.53, G.54, A.111, A.114, A.115, Y.119, N.311 Chain B: T.31, S.32, S.33, T.34, A.274, R.275, K.277 Ligands: MG.2 19 PLIP interactions: 12 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:S.33, B:T.34, B:R.275, B:K.277, A:N.25, A:N.25, A:K.52, A:M.53, A:M.53, A:Y.119 Water bridges: B:T.31, B:S.32, B:S.33, B:T.34, B:T.34, B:T.34, A:N.25 pi-Cation interactions: B:R.275, B:R.275 ACP.8: 17 residues within 4Å: Chain A: T.31, S.32, S.33, T.34, A.274, R.275, K.277 Chain B: N.25, K.52, M.53, G.54, A.111, A.114, A.115, Y.119, N.311 Ligands: MG.6 22 PLIP interactions: 14 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:S.33, A:T.34, A:T.34, A:R.275, A:K.277, B:N.25, B:N.25, B:K.52, B:M.53, B:M.53, B:Y.119 Water bridges: A:T.31, A:T.31, A:T.31, A:T.31, A:S.32, A:T.34, A:T.34, B:N.25, B:N.311 pi-Cation interactions: A:R.275, A:R.275

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

2005-11-01

Peptides

Hypothetical protein C320.14 in chromosome III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical protein C320.14 in chromosome III

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