SMTL ID : 7pxx.1

The crystal structure of Leishmania major Pteridine Reductase 1 in complex with substrate folic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

4 x FOL: FOLIC ACID(Non-covalent)

FOL.1: 11 residues within 4Å: Chain A: R.17, S.111, F.113, L.188, Y.191, Y.194, G.225, L.226, D.232, H.241 Ligands: NDP.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.113, A:L.188 Hydrogen bonds: A:R.17, A:S.111, A:Y.191, A:Y.194 Water bridges: A:G.225 pi-Stacking: A:F.113, A:F.113 FOL.4: 12 residues within 4Å: Chain B: R.17, S.111, F.113, L.188, Y.191, Y.194, G.225, L.226, L.229, M.233, H.241 Ligands: NDP.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.113, B:L.188, B:L.229 Hydrogen bonds: B:R.17, B:S.111, B:Y.194, B:Y.194 Water bridges: B:F.113 Salt bridges: B:H.241 pi-Stacking: B:F.113, B:F.113 FOL.11: 10 residues within 4Å: Chain C: R.17, S.111, F.113, L.188, Y.194, G.225, L.226, L.229, V.230 Ligands: NDP.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.188, C:L.229 Hydrogen bonds: C:R.17, C:S.111, C:Y.194 pi-Stacking: C:F.113, C:F.113, C:F.113 FOL.13: 11 residues within 4Å: Chain D: R.17, S.111, F.113, L.188, Y.191, Y.194, G.225, L.226, L.229, H.241 Ligands: NDP.14 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.113, D:L.188, D:L.229 Hydrogen bonds: D:R.17, D:S.111, D:Y.191, D:Y.194, D:Y.194 Water bridges: D:D.181, D:G.225 pi-Stacking: D:F.113, D:F.113

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

NDP.2: 28 residues within 4Å: Chain A: G.13, R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, A.110, S.111, S.112, D.142, S.146, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: FOL.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.17, A:L.18, A:H.38, A:R.39, A:S.40, A:D.65, A:L.66, A:S.67, A:N.109, A:S.111, A:S.111, A:S.111, A:D.142, A:D.142, A:K.198, A:S.227, A:S.227 Water bridges: A:A.15, A:A.15, A:R.17, A:N.109 Salt bridges: A:R.17, A:R.17 pi-Stacking: A:H.38 NDP.5: 27 residues within 4Å: Chain B: R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, A.110, S.111, S.112, D.142, S.146, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: FOL.4 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.17, B:L.18, B:H.38, B:H.38, B:R.39, B:S.40, B:D.65, B:L.66, B:S.67, B:N.109, B:S.111, B:S.111, B:S.111, B:Y.194, B:K.198, B:S.227, B:S.227 Water bridges: B:G.13, B:A.15, B:A.15, B:K.16, B:K.16, B:R.17, B:G.19, B:S.40, B:N.109, B:S.112, B:S.112 Salt bridges: B:R.17, B:R.17 pi-Stacking: B:H.38 NDP.12: 27 residues within 4Å: Chain C: G.13, R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, A.110, S.111, S.112, D.142, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: FOL.11 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:R.17, C:L.18, C:H.38, C:H.38, C:R.39, C:S.40, C:D.65, C:L.66, C:S.67, C:N.109, C:S.111, C:S.111, C:S.111, C:D.142, C:K.198, C:S.227, C:S.227 Water bridges: C:G.13, C:A.15, C:A.15, C:G.19, C:N.109 Salt bridges: C:R.17, C:R.17 pi-Cation interactions: C:H.38 NDP.14: 26 residues within 4Å: Chain D: R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, A.110, S.111, S.112, D.142, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: FOL.13 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.17, D:L.18, D:H.38, D:H.38, D:R.39, D:S.40, D:L.66, D:S.67, D:N.109, D:S.111, D:S.111, D:S.111, D:D.142, D:Y.194, D:K.198, D:S.227, D:S.227 Water bridges: D:G.13, D:A.15, D:G.19, D:R.39, D:S.40, D:S.40, D:N.109 Salt bridges: D:R.17, D:R.17 pi-Stacking: D:H.38

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

PGE.3: 5 residues within 4Å: Chain A: Y.248, R.250 Chain C: T.172, Q.216, K.270 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.172, C:K.270, A:Y.248, A:R.250 Water bridges: A:Y.248 PGE.6: 4 residues within 4Å: Chain A: L.189 Chain B: L.210, E.211, P.214 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain B: T.71, A.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.72, B:A.72 GOL.8: 1 residues within 4Å: Chain B: S.243 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.249 GOL.9: 6 residues within 4Å: Chain A: P.117, L.118, L.119, R.120 Chain B: K.156, H.160 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.156, A:L.118 Water bridges: B:K.156 GOL.15: 4 residues within 4Å: Chain B: Y.248, R.250 Chain D: Q.216, K.270 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Q.216, D:K.270, D:K.270, B:R.250 Water bridges: B:Y.248

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

PEG.10: 7 residues within 4Å: Chain A: N.68, I.149 Chain B: N.68, T.140, A.141, F.144, I.149 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.140, A:N.68 Water bridges: A:N.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dello Iacono, L. et al., Crystal structure of the ternary complex of Leishmania major pteridine reductase 1 with the cofactor NADP + /NADPH and the substrate folic acid. Acta Crystallogr.,Sect.F (2022)

Release Date

2022-04-06

Peptides

Pteridine reductase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase 1

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