SMTL ID : 1e7w.1

ONE ACTIVE SITE, TWO MODES OF REDUCTION CORRELATE THE MECHANISM OF LEISHMANIA PTERIDINE REDUCTASE WITH PTERIN METABOLISM AND ANTIFOLATE DRUG RESISTANCE IN TRPANOSOMES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: R.20, L.21, H.39, Y.40, H.41, R.42, S.43, A.67, D.68, L.69, S.70, N.112, A.113, S.114, S.115, D.145, M.182, V.183, D.184, Y.197, K.201, P.227, G.228, L.229, S.230 Ligands: MTX.2, EDO.4 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:D.184, A:P.227 Hydrogen bonds: A:K.19, A:K.19, A:R.20, A:L.21, A:H.41, A:R.42, A:S.43, A:L.69, A:S.70, A:N.112, A:S.114, A:S.114, A:S.114, A:D.145, A:Y.197, A:K.201, A:S.230, A:S.230 Water bridges: A:R.20, A:G.22, A:S.43, A:N.112 Salt bridges: A:R.20, A:R.20 pi-Stacking: A:H.41 NDP.5: 27 residues within 4Å: Chain B: G.16, R.20, L.21, H.39, Y.40, H.41, R.42, S.43, A.67, D.68, L.69, S.70, N.112, A.113, S.114, S.115, D.145, M.182, V.183, D.184, Y.197, K.201, P.227, G.228, L.229, S.230 Ligands: MTX.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:P.227 Hydrogen bonds: B:R.20, B:L.21, B:H.41, B:R.42, B:S.43, B:D.68, B:L.69, B:S.70, B:N.112, B:S.114, B:S.114, B:S.114, B:D.145, B:K.201, B:S.230, B:S.230 Water bridges: B:R.20, B:G.22, B:S.43, B:N.112, B:S.114 Salt bridges: B:R.20, B:R.20 pi-Stacking: B:H.41 NDP.8: 27 residues within 4Å: Chain C: R.20, L.21, H.39, Y.40, H.41, R.42, S.43, A.67, D.68, L.69, S.70, N.112, A.113, S.114, S.115, D.145, M.182, V.183, D.184, Y.197, K.201, P.227, G.228, L.229, S.230 Ligands: MTX.9, EDO.11 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:D.184, C:P.227 Hydrogen bonds: C:K.19, C:K.19, C:R.20, C:L.21, C:H.41, C:R.42, C:S.43, C:L.69, C:S.70, C:N.112, C:S.114, C:S.114, C:S.114, C:D.145, C:Y.197, C:K.201, C:S.230, C:S.230 Water bridges: C:A.18, C:A.18, C:R.20, C:G.22, C:S.43, C:N.112 Salt bridges: C:R.20, C:R.20 pi-Stacking: C:H.41 NDP.12: 27 residues within 4Å: Chain D: G.16, R.20, L.21, H.39, Y.40, H.41, R.42, S.43, A.67, D.68, L.69, S.70, N.112, A.113, S.114, S.115, D.145, M.182, V.183, D.184, Y.197, K.201, P.227, G.228, L.229, S.230 Ligands: MTX.13 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.227 Hydrogen bonds: D:R.20, D:L.21, D:H.41, D:R.42, D:S.43, D:D.68, D:L.69, D:S.70, D:N.112, D:S.114, D:S.114, D:S.114, D:D.145, D:K.201, D:S.230, D:S.230 Water bridges: D:R.20, D:G.22, D:S.43, D:N.112, D:S.114 Salt bridges: D:R.20, D:R.20 pi-Stacking: D:H.41

4 x MTX: METHOTREXATE(Non-covalent)

MTX.2: 15 residues within 4Å: Chain A: R.20, S.114, F.116, P.118, D.184, L.191, L.192, Y.194, Y.197, L.229, L.232, D.235, M.236 Ligands: NDP.1, EDO.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.191 Hydrogen bonds: A:R.20, A:S.114, A:S.114, A:Y.194, A:Y.194, A:Y.197, A:Y.197, A:D.235 Water bridges: A:R.20, A:R.20, A:D.235 pi-Stacking: A:F.116, A:F.116 MTX.6: 15 residues within 4Å: Chain B: R.20, S.114, F.116, P.118, D.184, L.191, L.192, Y.194, Y.197, G.228, L.229, W.241, H.244 Ligands: NDP.5, EDO.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.116, B:L.191, B:Y.194 Hydrogen bonds: B:R.20, B:S.114, B:S.114, B:Y.194, B:Y.197 pi-Stacking: B:F.116, B:F.116, B:W.241 MTX.9: 15 residues within 4Å: Chain C: R.20, S.114, F.116, P.118, D.184, L.191, L.192, Y.194, Y.197, L.229, L.232, D.235, M.236 Ligands: NDP.8, EDO.11 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.191 Hydrogen bonds: C:R.20, C:S.114, C:S.114, C:Y.194, C:Y.194, C:Y.197, C:Y.197, C:D.235 Water bridges: C:R.20, C:R.20, C:D.235 pi-Stacking: C:F.116, C:F.116 MTX.13: 15 residues within 4Å: Chain D: R.20, S.114, F.116, P.118, D.184, L.191, L.192, Y.194, Y.197, G.228, L.229, W.241, H.244 Ligands: NDP.12, EDO.14 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.116, D:L.191, D:Y.194 Hydrogen bonds: D:R.20, D:S.114, D:S.114, D:Y.194, D:Y.197 pi-Stacking: D:F.116, D:F.116, D:W.241

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

EDO.3: 6 residues within 4Å: Chain A: G.202, E.205, R.209 Chain B: G.202, E.205, R.209 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.205, A:R.209, A:R.209, B:R.209 Water bridges: B:R.209 EDO.4: 8 residues within 4Å: Chain A: F.116, D.184, T.187, L.191, Y.197 Chain D: R.290 Ligands: NDP.1, MTX.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.290 EDO.7: 6 residues within 4Å: Chain B: F.116, D.184, L.191, Y.197 Chain C: R.290 Ligands: MTX.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.290, C:R.290 Water bridges: B:L.191 EDO.10: 6 residues within 4Å: Chain C: G.202, E.205, R.209 Chain D: G.202, E.205, R.209 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.205, C:R.209, C:R.209, D:R.209 Water bridges: D:R.209 EDO.11: 8 residues within 4Å: Chain B: R.290 Chain C: F.116, D.184, T.187, L.191, Y.197 Ligands: NDP.8, MTX.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.290 EDO.14: 6 residues within 4Å: Chain A: R.290 Chain D: F.116, D.184, L.191, Y.197 Ligands: MTX.13 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Water bridges: D:L.191 Hydrogen bonds: A:R.290, A:R.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gourley, D.G. et al., Pteridine Reductase Mechanism Correlates Pterin Metabolism with Drug Resistance in Trypanosomatid Parasites. Nat.Struct.Biol. (2001)

Release Date

2001-09-06

Peptides

PTERIDINE REDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PTERIDINE REDUCTASE

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