SMTL ID : 5yx1.1 (1 other biounit)

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.95, D.96 No protein-ligand interaction detected (PLIP)

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.2: 12 residues within 4Å: Chain A: Y.7, F.8, R.13, W.38, K.42, G.48, K.49, I.50, P.51, Q.62, S.63 Chain B: D.96 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.49 Hydrogen bonds: A:I.50, A:I.50, A:Q.62, A:S.63, B:D.96 Water bridges: A:K.49, A:I.50, A:Q.62, A:S.63, A:S.63, A:L.64 Salt bridges: A:K.42, A:K.49 GSH.3: 11 residues within 4Å: Chain A: D.96 Chain B: Y.7, R.13, W.38, G.48, K.49, I.50, P.51, Q.62, S.63 Ligands: UX4.4 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.49 Hydrogen bonds: B:R.13, B:I.50, B:I.50, B:Q.62, B:S.63, A:D.96 Water bridges: B:R.13, B:Q.62, B:Q.62, B:S.63, B:L.64, B:D.95 Salt bridges: B:K.42, B:K.49

1 x UX4: ethyl 4-[(8R)-3,8-dimethyl-4-oxo-4,6,7,8,9,10-hexahydrothieno[2',3':4,5]pyrimido[1,2-a]azepin-2-yl]carbamoylpiperazine-1-carboxylate(Non-covalent)

UX4.4: 12 residues within 4Å: Chain B: M.10, G.12, R.13, Q.35, W.38, M.98, W.103, A.104, Y.151, I.154, T.158 Ligands: GSH.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.38, B:A.104, B:Y.151, B:I.154 Hydrogen bonds: B:T.158

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain B: R.11, Q.195, T.196, K.197 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.11, B:T.196 Water bridges: B:R.193, B:R.193, B:R.193, B:R.193, B:R.193, B:P.194, B:T.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaka, K. et al., Crystal structure of hematopoietic prostaglandin D synthase in complex with U004. 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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