SMTL ID : 1p33.1

Pteridine reductase from Leishmania tarentolae complex with NADPH and MTX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-tetramer

Ligands

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

NDP.1: 29 residues within 4Å: Chain A: G.14, K.17, R.18, L.19, Y.38, H.39, R.40, S.41, A.65, D.66, L.67, S.68, N.110, A.111, S.112, S.113, D.143, S.147, M.180, V.181, D.182, Y.195, K.199, P.225, G.226, L.227, S.228, V.229 Ligands: MTX.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.225 Hydrogen bonds: A:R.18, A:L.19, A:H.39, A:R.40, A:S.41, A:L.67, A:S.68, A:N.110, A:N.110, A:S.112, A:S.112, A:S.112, A:D.143, A:S.147, A:Y.195, A:K.199, A:S.228, A:V.229 Salt bridges: A:R.18, A:R.18 pi-Stacking: A:H.39 NDP.3: 30 residues within 4Å: Chain B: G.14, A.16, K.17, R.18, L.19, H.37, Y.38, H.39, R.40, S.41, A.65, D.66, L.67, S.68, N.110, A.111, S.112, S.113, D.143, S.147, M.180, V.181, D.182, Y.195, K.199, P.225, G.226, S.228, V.229 Ligands: MTX.4 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:R.18, B:L.19, B:H.39, B:R.40, B:S.41, B:D.66, B:L.67, B:S.68, B:N.110, B:S.112, B:S.112, B:S.112, B:D.143, B:Y.195, B:K.199, B:S.228, B:V.229 Water bridges: B:N.110 Salt bridges: B:R.18, B:R.18 pi-Stacking: B:H.39 NDP.5: 29 residues within 4Å: Chain C: G.14, A.16, R.18, L.19, Y.38, H.39, R.40, S.41, A.65, D.66, L.67, S.68, N.110, A.111, S.112, S.113, D.143, S.147, M.180, V.181, D.182, Y.195, K.199, P.225, G.226, L.227, S.228, V.229 Ligands: MTX.6 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.225 Hydrogen bonds: C:L.19, C:H.39, C:R.40, C:S.41, C:L.67, C:S.68, C:N.110, C:S.112, C:S.112, C:S.112, C:D.143, C:D.143, C:S.147, C:K.199, C:S.228, C:V.229 Water bridges: C:N.110 Salt bridges: C:K.17, C:K.17, C:R.18, C:R.18 pi-Stacking: C:H.39 NDP.7: 29 residues within 4Å: Chain D: G.14, A.16, K.17, R.18, L.19, Y.38, H.39, R.40, S.41, A.65, D.66, L.67, S.68, N.110, A.111, S.112, S.113, D.143, S.147, M.180, V.181, Y.195, K.199, P.225, G.226, L.227, S.228, V.229 Ligands: MTX.8 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:P.225 Hydrogen bonds: D:K.17, D:R.18, D:L.19, D:H.39, D:R.40, D:S.41, D:D.66, D:L.67, D:S.68, D:N.110, D:S.112, D:S.112, D:S.112, D:D.143, D:D.143, D:K.199, D:S.228, D:V.229 Salt bridges: D:K.17, D:K.17, D:R.18, D:R.18 pi-Stacking: D:H.39

4 x MTX: METHOTREXATE(Non-covalent)

MTX.2: 14 residues within 4Å: Chain A: R.18, S.112, F.114, P.116, D.182, L.189, Y.192, Y.195, L.227, L.230, P.231, M.234, Y.242 Ligands: NDP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.189, A:P.231, A:Y.242 Hydrogen bonds: A:R.18, A:S.112, A:S.112, A:D.182, A:Y.195, A:Y.195, A:Y.242 Water bridges: A:Y.192, A:Y.192 pi-Stacking: A:F.114, A:F.114 MTX.4: 14 residues within 4Å: Chain B: R.18, S.112, F.114, P.116, D.182, L.189, Y.192, Y.195, L.227, L.230, P.231, M.234, Y.242 Ligands: NDP.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.189, B:P.231 Hydrogen bonds: B:R.18, B:S.112, B:S.112, B:Y.192, B:Y.192, B:Y.195, B:Y.195 pi-Stacking: B:F.114, B:F.114 MTX.6: 14 residues within 4Å: Chain C: R.18, S.112, F.114, P.116, D.182, L.189, Y.192, Y.195, L.227, L.230, P.231, M.234, Y.242 Ligands: NDP.5 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.189, C:P.231 Hydrogen bonds: C:R.18, C:S.112, C:Y.192, C:Y.192, C:Y.195, C:Y.242 pi-Stacking: C:F.114, C:F.114, C:Y.242 MTX.8: 13 residues within 4Å: Chain D: R.18, S.112, F.114, P.116, D.182, L.189, Y.192, Y.195, L.230, P.231, M.234, Y.242 Ligands: NDP.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.189, D:P.231, D:Y.242 Hydrogen bonds: D:R.18, D:S.112, D:S.112, D:Y.192, D:Y.192, D:Y.195 pi-Stacking: D:F.114, D:F.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, H. et al., Structure of pteridine reductase (PTR1) from Leishmania tarentolae. Acta Crystallogr.,Sect.D (2003)

Release Date

2003-09-02

Peptides

Pteridine reductase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase 1