SMTL ID : 3hbb.2 (1 other biounit)

Structures of dihydrofolate reductase-thymidylate synthase of Trypanosoma cruzi in the folate-free state and in complex with two antifolate drugs, trimetrexate and methotrexate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 25 residues within 4Å: Chain A: A.28, I.35, G.38, R.39, S.40, I.41, W.43, G.77, R.78, K.79, T.80, L.99, S.100, S.101, T.102, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: TMQ.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.80, A:Y.160 Hydrogen bonds: A:A.28, A:I.35, A:G.38, A:G.77, A:R.78, A:K.79, A:K.79, A:T.80, A:S.101, A:S.101, A:T.102, A:G.157, A:S.158, A:S.158 Salt bridges: A:R.78, A:K.79 NAP.10: 26 residues within 4Å: Chain B: V.27, A.28, I.35, G.36, G.38, R.39, S.40, I.41, G.77, R.78, K.79, T.80, L.99, S.100, S.101, T.102, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: TMQ.11 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.80 Hydrogen bonds: B:A.28, B:I.35, B:G.38, B:G.38, B:R.39, B:G.77, B:R.78, B:R.78, B:K.79, B:T.80, B:S.101, B:T.102, B:G.157, B:S.158, B:S.158, B:V.159 Salt bridges: B:R.78, B:K.79

2 x TMQ: TRIMETREXATE(Non-covalent)

TMQ.2: 12 residues within 4Å: Chain A: V.26, V.27, A.28, I.41, D.48, F.52, T.80, S.83, F.88, I.154, Y.160 Ligands: NAP.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.41, A:T.80 Hydrogen bonds: A:V.26, A:V.27 Salt bridges: A:D.48 TMQ.11: 15 residues within 4Å: Chain B: V.26, V.27, A.28, I.41, D.48, M.49, F.52, S.83, I.84, P.85, L.91, I.154, Y.160, T.178 Ligands: NAP.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.41, B:F.52 Hydrogen bonds: B:V.26, B:Y.160, B:T.178, B:T.178 Salt bridges: B:D.48

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.323, E.335, E.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.336 Water bridges: A:R.323 Salt bridges: A:R.323 SO4.4: 4 residues within 4Å: Chain A: R.491, R.493, E.494, D.498 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.494, A:D.498, A:D.498 Salt bridges: A:R.491, A:R.493 SO4.5: 3 residues within 4Å: Chain A: A.352, Q.364, G.365 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.365 SO4.6: 2 residues within 4Å: Chain A: R.233, R.235 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.233, A:R.235 SO4.7: 2 residues within 4Å: Chain A: F.288, R.290 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.290 SO4.9: 5 residues within 4Å: Chain A: R.383, R.384 Chain B: R.257, R.423, S.424 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.383, A:R.384, B:R.423 Hydrogen bonds: B:S.424 SO4.12: 5 residues within 4Å: Chain A: R.257, R.423, S.424 Chain B: R.383, R.384 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.257, A:S.424 Salt bridges: A:R.423, B:R.383, B:R.384 Water bridges: B:R.383, B:R.384 SO4.13: 3 residues within 4Å: Chain B: R.60, V.506 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.60 SO4.14: 3 residues within 4Å: Chain B: R.39, R.78, K.79 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.39, B:R.78, B:K.79 SO4.15: 8 residues within 4Å: Chain A: F.350, G.351, N.391, S.393 Chain B: F.350, G.351, N.391, S.393 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.351, B:N.391, B:S.393, A:N.391, A:S.393 SO4.16: 3 residues within 4Å: Chain B: F.288, R.290 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.290 SO4.17: 2 residues within 4Å: Chain B: R.233, R.235 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.233, B:R.235 SO4.18: 4 residues within 4Å: Chain B: R.491, R.493, E.494, D.498 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.494, B:D.498 Water bridges: B:R.491, B:R.491 Salt bridges: B:R.491, B:R.493 SO4.19: 3 residues within 4Å: Chain B: R.323, E.335, E.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.336 Salt bridges: B:R.323

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

EDO.8: 3 residues within 4Å: Chain A: N.252, V.253 Chain B: N.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.252, A:V.253, A:V.253 EDO.20: 4 residues within 4Å: Chain B: R.286, V.506, Y.509 Ligands: SO4.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.286 EDO.21: 4 residues within 4Å: Chain B: R.286, V.287, F.288 Ligands: SO4.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.289 EDO.22: 6 residues within 4Å: Chain B: Q.173, A.174, K.229, I.231, R.482, A.510 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.229 EDO.23: 3 residues within 4Å: Chain A: N.413 Chain B: N.252, V.253 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.253, A:N.413, A:N.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Senkovich, O. et al., Structures of dihydrofolate reductase-thymidylate synthase of Trypanosoma cruzi in the folate-free state and in complex with two antifolate drugs, trimetrexate and methotrexate. Acta Crystallogr.,Sect.D (2009)

Release Date

2009-05-19

Peptides

Dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Dihydrofolate reductase-thymidylate synthase

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