SMTL ID : 3anv.1

Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 15 residues within 4Å: Chain A: H.43, K.45, A.86, R.143, Y.174, H.176, Y.181, S.221, T.222, P.223, H.239, P.240, G.241, N.242 Ligands: 2RA.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.174 Hydrogen bonds: A:R.143, A:Y.174, A:T.222, A:T.222, A:G.241, A:N.242 Water bridges: A:N.242 Salt bridges: A:K.45, A:H.176 pi-Stacking: A:H.176 PLP.5: 15 residues within 4Å: Chain B: H.43, K.45, A.86, R.143, Y.174, H.176, Y.181, S.221, T.222, P.223, H.239, P.240, G.241, N.242 Ligands: 2RA.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.174 Hydrogen bonds: B:R.143, B:Y.174, B:T.222, B:T.222, B:G.241, B:N.242 Water bridges: B:N.242 Salt bridges: B:K.45, B:H.176 pi-Stacking: B:H.176

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 7 residues within 4Å: Chain A: S.289, L.290, H.291 Chain B: S.289, L.290, H.291 Ligands: CL.6 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain A: S.289, L.290, H.291 Chain B: S.289, L.290, H.291 Ligands: CL.2 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.347, C.349 Ligands: 2RA.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.347, A:C.349, H2O.3, H2O.4, H2O.4 ZN.7: 3 residues within 4Å: Chain B: H.347, C.349 Ligands: 2RA.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.347, B:C.349, H2O.7, H2O.7, H2O.7

2 x 2RA: 3-amino-D-alanine(Non-covalent)

2RA.4: 9 residues within 4Å: Chain A: K.45, R.143, H.176, H.347 Chain B: W.285, T.317, Q.318 Ligands: PLP.1, ZN.3 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.317, B:T.317, B:Q.318, B:Q.318, A:K.45, A:R.143, A:H.176 Salt bridges: A:K.45, A:H.347 2RA.8: 9 residues within 4Å: Chain A: W.285, T.317, Q.318 Chain B: K.45, R.143, H.176, H.347 Ligands: PLP.5, ZN.7 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.317, A:T.317, A:Q.318, A:Q.318, B:K.45, B:R.143, B:H.176 Salt bridges: B:K.45, B:H.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, H. et al., Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney. J.Biol.Chem. (2011)

Release Date

2011-06-15

Peptides

D-serine dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

D-serine dehydratase

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