SMTL ID : 2x9v.1

High resolution structure of TbPTR1 with trimetrexate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 27 residues within 4Å: Chain A: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: TMQ.2 31 PLIP interactions: 31 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:D.82, A:L.83, A:T.84, A:T.84, A:N.113, A:S.115, A:S.115, A:S.115, A:Y.194, A:K.198, A:S.227, A:L.228 Water bridges: A:A.32, A:R.34, A:R.34, A:G.36, A:H.55, A:H.55, A:S.57, A:S.57, A:N.113, A:S.115 Salt bridges: A:R.34, A:R.34 NAP.4: 26 residues within 4Å: Chain B: R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: TMQ.5 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.34, B:I.35, B:H.55, B:H.55, B:N.56, B:N.56, B:S.57, B:D.82, B:D.82, B:L.83, B:T.84, B:N.113, B:S.115, B:S.115, B:S.115, B:Y.194, B:K.198, B:S.227, B:L.228 Water bridges: B:G.36, B:S.57, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.8: 26 residues within 4Å: Chain C: R.34, I.35, 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, Y.194, K.198, P.224, G.225, V.226, S.227 Ligands: TMQ.9 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:R.34, C:I.35, C:H.55, C:N.56, C:N.56, C:S.57, C:D.82, C:L.83, C:T.84, C:N.113, C:S.115, C:S.115, C:S.115, C:K.198, C:S.227, C:S.227 Water bridges: C:R.34, C:G.36, C:S.57, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 NAP.12: 25 residues within 4Å: Chain D: R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227 Ligands: TMQ.13 26 PLIP interactions: 26 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:D.82, D:D.82, D:L.83, D:T.84, D:N.113, D:S.115, D:S.115, D:S.115, D:K.198, D:S.227, D:S.227 Water bridges: D:R.34, D:G.36, D:S.57, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x TMQ: TRIMETREXATE(Non-covalent)

TMQ.2: 13 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, C.188, Y.194, L.228, L.229, P.230, M.233, E.237, W.241 Ligands: NAP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.117, A:F.117 Hydrogen bonds: A:S.115, A:S.115, A:Y.194, A:Y.194 Water bridges: A:E.237 pi-Stacking: A:F.117, A:F.117 TMQ.5: 11 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, C.188, Y.194, L.228, L.229, P.230, M.233 Ligands: NAP.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.117, B:F.117, B:P.230 Hydrogen bonds: B:S.115, B:S.115, B:Y.194, B:Y.194 Water bridges: B:E.237 pi-Stacking: B:F.117, B:F.117 TMQ.9: 11 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, C.188, F.191, Y.194, L.229, P.230, M.233 Ligands: NAP.8 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.117 Hydrogen bonds: C:S.115, C:S.115, C:Y.194 Water bridges: C:Y.194 pi-Stacking: C:F.117, C:F.117, C:F.117 TMQ.13: 10 residues within 4Å: Chain D: S.115, F.117, D.181, C.188, F.191, Y.194, L.229, P.230, M.233 Ligands: NAP.12 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.117, D:F.117 Hydrogen bonds: D:S.115, D:Y.194 Water bridges: D:Y.194 pi-Stacking: D:F.117, D:F.117

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

ACT.3: 4 residues within 4Å: Chain A: Q.206, G.274, I.276 Chain B: K.278 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.206, A:I.276 Hydrogen bonds: A:Q.206, A:G.274 Water bridges: B:K.278, B:K.278 Salt bridges: B:K.278 ACT.6: 5 residues within 4Å: Chain B: V.231, A.232, M.233, G.234, E.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.235 Water bridges: B:K.238, B:K.238 Salt bridges: B:K.238 ACT.7: 4 residues within 4Å: Chain A: K.278 Chain B: Q.206, G.274, I.276 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Q.206, B:I.276 Hydrogen bonds: B:Q.206 Water bridges: B:I.276, A:K.278, A:K.278 Salt bridges: A:K.278 ACT.10: 4 residues within 4Å: Chain C: Q.206, G.274, I.276 Chain D: K.278 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Q.206, C:I.276 Hydrogen bonds: C:Q.206 Water bridges: D:K.278, D:K.278 Salt bridges: D:K.278 ACT.11: 2 residues within 4Å: Chain C: V.77, V.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.78 Water bridges: C:N.69 ACT.14: 4 residues within 4Å: Chain C: K.278 Chain D: Q.206, G.274, I.276 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Q.206, D:I.276 Hydrogen bonds: D:Q.206 Water bridges: D:I.276, C:K.278, C:K.278 Salt bridges: C:K.278

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

2010-06-23

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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