SMTL ID : 9d6z.1

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (Orthorhombic C form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: T.37, N.38, S.39 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: H.31, K.77, E.78 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: Q.85, L.105, A.106, S.107, D.120 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: A.168, A.169, A.170, V.192, G.193 Ligands: DMS.7 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: K.184 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: V.290 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: N.167, A.168, A.191, Y.212, V.237 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: A.168, A.169, A.170, V.192, K.197 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: Y.200, K.203, K.318 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: K.184 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: G.34, R.70, R.266 Ligand excluded by PLIP

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 5 residues within 4Å: Chain A: Y.35, I.261, L.336, K.337, G.338 No protein-ligand interaction detected (PLIP) DMS.7: 9 residues within 4Å: Chain A: N.167, A.168, A.191, V.192, G.193, Y.212, V.237, F.241 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.168 pi-Cation interactions: A:Y.212 DMS.16: 7 residues within 4Å: Chain A: Y.68, V.71, R.75 Chain B: E.277, I.280, Y.281 Ligands: MTX.8 No protein-ligand interaction detected (PLIP) DMS.17: 6 residues within 4Å: Chain B: Q.85, L.105, A.106, S.107, D.120, E.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.85 Salt bridges: B:D.120

2 x MTX: METHOTREXATE(Non-covalent)

MTX.8: 18 residues within 4Å: Chain A: D.66, P.67, Y.68, A.72, R.75, M.143, P.144, T.147, G.171, A.172, V.173, V.291, Y.292, M.335, G.342, K.343, T.344 Ligands: DMS.16 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:D.66, A:P.144 Hydrogen bonds: A:D.66, A:R.75, A:R.75, A:A.172, A:V.173, A:T.344 Water bridges: A:Y.68, A:Y.68, A:G.171, A:M.335, A:N.340 Salt bridges: A:K.343 pi-Stacking: A:Y.68, A:Y.68 MTX.18: 18 residues within 4Å: Chain A: Y.281 Chain B: D.66, P.67, Y.68, A.72, R.75, M.143, P.144, T.147, G.171, A.172, V.173, V.290, V.291, Y.292, M.335, K.343, T.344 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.66, B:Y.68, B:P.144, B:K.343 Hydrogen bonds: B:D.66, B:D.66, B:R.75, B:R.75, B:A.172, B:V.173, B:Y.292, B:Y.292, B:T.344, A:Y.281 Water bridges: B:G.171, B:G.171 Salt bridges: B:K.343 pi-Stacking: B:Y.68, B:Y.68

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 2 residues within 4Å: Chain A: R.293 Chain B: F.252 No protein-ligand interaction detected (PLIP) PEG.19: 3 residues within 4Å: Chain A: F.252 Chain B: R.293, W.294 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Enayati, P. et al., Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (Orthorhombic C form). To be published

Release Date

2025-08-20

Peptides

Prostaglandin reductase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin reductase 1

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