SMTL ID : 2x9g.1

High resolution structure of TbPTR1 in complex with Pemetrexed

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 31 residues within 4Å: Chain A: G.30, K.33, R.34, I.35, G.36, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, A.116, T.146, L.179, C.180, D.181, A.182, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: LYA.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, A:N.56, A:N.56, A:S.57, A:L.83, A:T.84, A:T.84, A:T.84, A:S.115, A:S.115, A:L.179, A:Y.194, A:K.198, A:K.198, A:S.227, A:L.228 Water bridges: A:G.30, A:G.30, A:R.34, A:R.34, A:G.36, A:S.57, A:S.57, A:N.113 Salt bridges: A:R.34, A:R.34 NAP.3: 32 residues within 4Å: Chain B: G.30, A.32, K.33, R.34, I.35, G.36, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, A.116, T.146, L.179, C.180, D.181, A.182, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: LYA.4 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.34, B:I.35, B:H.55, B:N.56, B:N.56, B:S.57, B:D.82, B:L.83, B:T.84, B:T.84, B:S.115, B:L.179, B:Y.194, B:K.198, B:K.198, B:S.227, B:L.228 Water bridges: B:G.30, B:R.34, B:R.34, B:G.36, B:H.55, B:S.57, B:N.113, B:E.142 Salt bridges: B:R.34, B:R.34 NAP.6: 31 residues within 4Å: Chain C: G.30, K.33, R.34, I.35, G.36, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, A.116, T.146, L.179, C.180, D.181, A.182, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: LYA.7 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:I.35, C:H.55, C:N.56, C:N.56, C:S.57, C:L.83, C:T.84, C:S.115, C:S.115, C:L.179, C:K.198, C:S.227, C:L.228 Water bridges: C:G.30, C:A.32, C:R.34, C:R.34, C:R.34, C:G.36, C:H.55, C:S.57, C:S.57, C:N.113, C:E.142, C:K.198 Salt bridges: C:R.34, C:R.34 NAP.8: 32 residues within 4Å: Chain D: G.30, A.32, K.33, R.34, I.35, G.36, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, A.116, T.146, L.179, C.180, D.181, A.182, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: LYA.9 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.34, D:I.35, D:H.55, D:N.56, D:N.56, D:S.57, D:S.57, D:D.82, D:L.83, D:T.84, D:T.84, D:S.115, D:L.179, D:K.198, D:S.227, D:L.228 Water bridges: D:G.30, D:K.33, D:K.33, D:R.34, D:G.36, D:T.84, D:N.113, D:K.198 Salt bridges: D:R.34, D:R.34

4 x LYA: 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID(Non-covalent)

LYA.2: 16 residues within 4Å: Chain A: R.34, S.115, F.117, P.119, D.181, C.188, F.191, Y.194, V.226, L.228, L.229, P.230, M.233, E.237, W.241 Ligands: NAP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.230, A:W.241 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194, A:Y.194 Water bridges: A:R.34, A:R.34, A:F.117, A:W.241 pi-Stacking: A:F.117, A:F.117, A:F.117 LYA.4: 16 residues within 4Å: Chain B: R.34, S.115, F.117, P.119, D.181, C.188, F.191, Y.194, V.226, L.228, L.229, P.230, M.233, E.237, W.241 Ligands: NAP.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.230, B:W.241 Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194, B:Y.194 Water bridges: B:R.34, B:R.34, B:F.117, B:W.241 pi-Stacking: B:F.117, B:F.117, B:F.117 LYA.7: 15 residues within 4Å: Chain C: R.34, S.115, F.117, P.119, D.181, C.188, F.191, Y.194, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.117, C:P.119, C:F.191, C:P.230, C:W.241 Hydrogen bonds: C:S.115, C:S.115, C:Y.194 Water bridges: C:R.34, C:R.34, C:F.117 pi-Stacking: C:F.117, C:F.117 LYA.9: 17 residues within 4Å: Chain D: R.34, S.115, F.117, P.119, D.181, C.188, F.191, Y.194, V.226, S.227, L.228, L.229, P.230, M.233, E.237, W.241 Ligands: NAP.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.117, D:P.119, D:F.191, D:P.230, D:W.241 Hydrogen bonds: D:R.34, D:S.115, D:Y.194 Water bridges: D:R.34, D:R.34, D:F.117 pi-Stacking: D:F.117, D:F.117

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain B: A.232, M.233, G.234, E.235 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.235 Water bridges: B:K.238, B:K.238, B:K.238 Salt bridges: B:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., High-Resolution Structures of Trypanosoma Brucei Pteridine Reductase Ligand Complexes Inform on the Placement of New Molecular Entities in the Active Site of a Potential Drug Target. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-06-16

Peptides

PTERIDINE REDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PTERIDINE REDUCTASE

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