SMTL ID : 2bf7.1

Leishmania major pteridine reductase 1 in complex with NADP and biopterin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 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: HBI.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.17, A:L.18, A:H.38, A:H.38, A:R.39, A:S.40, A:D.65, A:L.66, A:N.109, A:S.111, A:S.111, A:S.111, A:Y.194, A:K.198, A:S.227, A:S.227 Water bridges: A:G.19, A:N.109 Salt bridges: A:R.17, A:R.17 pi-Stacking: A:H.38 NAP.4: 28 residues within 4Å: Chain B: 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: HBI.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:K.16, B:R.17, B:L.18, B:H.38, B:R.39, B:S.40, B:D.65, B:D.65, B:L.66, B:S.67, B:N.109, B:S.111, B:S.111, B:S.111, B:K.198, B:S.227, B:S.227 Water bridges: B:N.109, B:N.109 Salt bridges: B:R.17, B:R.17 pi-Stacking: B:H.38 NAP.7: 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: HBI.8 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:Y.194, 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-Stacking: C:H.38 NAP.11: 28 residues within 4Å: Chain D: G.13, K.16, 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: HBI.12 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.17, D:L.18, D:H.38, D:R.39, D:S.40, D:D.65, D:D.65, D:L.66, D:S.67, D:N.109, D:S.111, D:S.111, D:S.111, D:K.198, D:S.227, D:S.227 Water bridges: D:A.15, D:G.19, D:N.109 Salt bridges: D:K.16, D:R.17, D:R.17 pi-Stacking: D:H.38

4 x HBI: 7,8-DIHYDROBIOPTERIN(Non-covalent)

HBI.2: 9 residues within 4Å: Chain A: R.17, S.111, F.113, D.181, Y.194, G.225, L.226, L.229 Ligands: NAP.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.113 Hydrogen bonds: A:R.17, A:S.111, A:S.111, A:Y.194, A:G.225 pi-Stacking: A:F.113, A:F.113 Water bridges: D:R.287, D:R.287 HBI.5: 9 residues within 4Å: Chain B: R.17, S.111, F.113, D.181, Y.194, G.225, L.226, L.229 Ligands: NAP.4 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.229 Hydrogen bonds: B:R.17, B:S.111, B:S.111, B:G.225 pi-Stacking: B:F.113, B:F.113 Water bridges: C:R.287, C:R.287 HBI.8: 9 residues within 4Å: Chain C: R.17, S.111, F.113, D.181, L.188, Y.194, L.226, L.229 Ligands: NAP.7 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.226 Hydrogen bonds: C:R.17, C:S.111, C:S.111, C:Y.194 pi-Stacking: C:F.113, C:F.113 Water bridges: B:R.287 HBI.12: 8 residues within 4Å: Chain D: R.17, S.111, F.113, D.181, Y.194, L.226, L.229 Ligands: NAP.11 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain D Water bridges: A:R.287 Hydrogen bonds: D:R.17, D:S.111, D:S.111 pi-Stacking: D:F.113, D:F.113

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

EDO.3: 6 residues within 4Å: Chain A: G.199, E.202, R.206 Chain B: G.199, E.202, R.206 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.202, A:R.206, A:R.206, B:R.206 EDO.6: 3 residues within 4Å: Chain A: N.68 Chain B: N.68, F.144 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.68, A:N.68 EDO.9: 3 residues within 4Å: Chain C: N.52, P.56, N.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.57 Water bridges: C:N.52 EDO.10: 4 residues within 4Å: Chain C: N.68 Chain D: N.68, T.140, A.141 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.68, D:T.140, C:N.68 EDO.13: 6 residues within 4Å: Chain D: R.170, G.171, T.172, Y.174, L.215, Q.216 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.172, D:Q.216 Water bridges: D:R.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schuettelkopf, A.W. et al., Structures of Leishmania Major Pteridine Reductase Complexes Reveal the Active Site Features Important for Ligand Binding and to Guide Inhibitor Design. J.Mol.Biol. (2005)

Release Date

2005-08-31

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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