SMTL ID : 5ywe.1 (1 other biounit)

Crystal structure of hematopoietic prostaglandin D synthase apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 10 residues within 4Å: Chain A: Y.7, R.13, W.38, G.48, K.49, I.50, P.51, Q.62, S.63 Chain B: D.96 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.96, A:I.50, A:I.50, A:Q.62, A:S.63 Water bridges: B:D.92, B:D.92, A:Q.62, A:L.64 Salt bridges: A:R.13, A:K.42 GSH.5: 11 residues within 4Å: Chain A: D.96 Chain B: Y.7, R.13, W.38, K.42, G.48, K.49, I.50, P.51, Q.62, S.63 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.49 Hydrogen bonds: B:I.50, B:I.50, B:Q.62, B:Q.62, B:S.63, A:D.96 Water bridges: B:R.13, B:R.13, B:I.50, B:L.64 Salt bridges: B:R.13, B:K.42

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.11, Q.195, T.196, K.197 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.11, A:T.196, A:T.196 Water bridges: A:R.193, A:R.193, A:R.193, A:R.193 GOL.3: 3 residues within 4Å: Chain A: Q.27, Y.28, E.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.27 Water bridges: A:Y.28, A:Y.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain B: D.95 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaka, K. et al., Crystal structure of hematopoietic prostaglandin D synthase apo form. To Be Published

Release Date

2018-12-05

Peptides

Hematopoietic prostaglandin D synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hematopoietic prostaglandin D synthase

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