SMTL ID : 2x9n.1

High resolution structure of TbPTR1 in complex with cyromazine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: 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, L.228 Ligands: AX3.2, DTD.3 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:D.82, 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:G.36, A:H.55, A:H.55, A:H.55, A:S.57, A:N.113, A:S.115 Salt bridges: A:R.34, A:R.34 NAP.5: 28 residues within 4Å: Chain B: 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: AX3.6, D1D.7 25 PLIP interactions: 25 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:K.198, B:S.227, B:L.228 Water bridges: B:R.34, B:G.36, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 NAP.8: 29 residues within 4Å: Chain C: G.30, K.33, 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: AX3.9, DTD.10 28 PLIP interactions: 28 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:T.84, C:N.113, C:S.115, C:S.115, C:S.115, C:Y.194, C:K.198, C:S.227, C:L.228 Water bridges: C:K.33, C:R.34, C:G.36, C:H.55, C:H.55, C:S.57, C:N.113 Salt bridges: C:R.34, C:R.34 NAP.12: 28 residues within 4Å: Chain D: 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: AX3.13, D1D.14 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:H.55, D:N.56, D:N.56, D:S.57, 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:L.228 Water bridges: D:G.30, D:A.32, D:G.36, D:S.57, D:S.57, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34

4 x AX3: N~2~-cyclopropyl-1,3,5-triazine-2,4,6-triamine(Non-covalent)

AX3.2: 10 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230 Ligands: NAP.1, DTD.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.117, A:P.230 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194, A:Y.194 Water bridges: A:R.34 pi-Stacking: A:F.117 pi-Cation interactions: A:F.117 AX3.6: 8 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.5, D1D.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194 pi-Stacking: B:F.117 pi-Cation interactions: B:F.117 AX3.9: 8 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.8, DTD.10 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.230 Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:Y.194, C:Y.194 pi-Stacking: C:F.117 pi-Cation interactions: C:F.117 AX3.13: 8 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.12, D1D.14 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.230 Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117 pi-Cation interactions: D:F.117

2 x DTD: DITHIANE DIOL(Non-covalent)

DTD.3: 7 residues within 4Å: Chain A: D.181, C.188, G.225, L.229, W.241 Ligands: NAP.1, AX3.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.181 DTD.10: 7 residues within 4Å: Chain C: F.117, D.181, C.188, L.229, W.241 Ligands: NAP.8, AX3.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.181

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain A: N.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.56 Water bridges: A:A.58 NA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x D1D: (4S,5S)-1,2-DITHIANE-4,5-DIOL(Non-covalent)

D1D.7: 10 residues within 4Å: Chain B: F.117, D.181, C.188, G.225, V.226, L.229, M.233, W.241 Ligands: NAP.5, AX3.6 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.181, B:D.181, B:D.181, B:D.181 D1D.14: 11 residues within 4Å: Chain D: F.117, D.181, C.188, G.225, V.226, L.229, P.230, M.233, W.241 Ligands: NAP.12, AX3.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.181

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

ACT.11: 3 residues within 4Å: Chain C: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.34 Salt bridges: C:R.37

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

2010-06-30

Peptides

PTERIDINE REDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PTERIDINE REDUCTASE

Related Entries With Identical Sequence