SMTL ID : 5y9z.1

Crystal structure of rat hematopoietic prostaglandin D synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 11 residues within 4Å: Chain A: Y.8, R.14, W.39, K.43, K.50, I.51, P.52, Q.63, S.64 Chain B: D.97 Ligands: DIO.4 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.51, A:I.51, A:Q.63, A:S.64, B:D.97 Water bridges: A:R.14, A:R.14, A:Q.63, A:L.65 Salt bridges: A:R.14, A:K.43 GSH.10: 11 residues within 4Å: Chain A: D.97 Chain B: Y.8, R.14, W.39, K.43, K.50, I.51, P.52, Q.63, S.64 Ligands: DIO.12 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.50 Hydrogen bonds: B:I.51, B:I.51, B:Q.63, B:S.64, A:D.97 Water bridges: B:R.14, B:Q.63, B:L.65, B:D.96 Salt bridges: B:R.14, B:K.43

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

MG.2: 2 residues within 4Å: Chain A: D.96 Chain B: D.96 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.4: 6 residues within 4Å: Chain A: Y.8, G.13, W.104, L.199 Ligands: GSH.1, DIO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.8 Water bridges: A:G.13 DIO.5: 7 residues within 4Å: Chain A: G.13, R.14, M.99, Y.152, I.155, C.156 Ligands: DIO.4 No protein-ligand interaction detected (PLIP) DIO.11: 7 residues within 4Å: Chain B: G.13, R.14, M.99, Y.152, I.155, C.156 Ligands: DIO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.152 Water bridges: B:T.159, B:T.159 DIO.12: 6 residues within 4Å: Chain B: Y.8, G.13, W.104, L.199 Ligands: GSH.10, DIO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.8 Water bridges: B:G.13, B:R.14

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 2 residues within 4Å: Chain A: N.144 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.144 EDO.7: 4 residues within 4Å: Chain A: N.10, R.33, I.34, E.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.33 Water bridges: A:N.10, A:N.10 EDO.8: 3 residues within 4Å: Chain A: A.183, I.184, P.185 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain B: V.175, N.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.179 Water bridges: B:R.178

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: E.139, W.140, N.144, Y.145 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.140, A:K.180

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 4 residues within 4Å: Chain A: L.83 Chain B: V.56, E.57, Y.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.57 Water bridges: B:Y.70 PGE.14: 2 residues within 4Å: Chain B: Y.24, L.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.24 Water bridges: B:L.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kamo, M. et al., Crystal structure of rat hematopoietic prostaglandin D synthase. To Be Published

Release Date

2018-09-19

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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