SMTL ID : 3hbb.1 (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: 26 residues within 4Å: Chain A: 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.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.41, A:T.80 Hydrogen bonds: A:A.28, A:I.35, A:G.38, A:G.77, A:R.78, A:R.78, A:K.79, A:T.80, A:T.80, A:S.101, A:S.101, A:G.157, A:S.158, A:S.158, A:Y.160 Salt bridges: A:R.78 NAP.11: 26 residues within 4Å: Chain B: A.28, I.35, G.36, D.37, 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.12 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.80 Hydrogen bonds: B:A.28, B:I.35, B:D.37, B:D.37, B:D.37, B:G.38, B:G.77, B:R.78, B:R.78, B:K.79, B:T.80, B:T.80, B:S.83, B:S.83, B:S.100, B:S.101, B:T.102, B:G.156, B:G.157, B:S.158, B:S.158, B:V.159, B:Y.160 Salt bridges: B:R.78, B:K.79

2 x TMQ: TRIMETREXATE(Non-covalent)

TMQ.2: 13 residues within 4Å: Chain A: V.26, V.27, A.28, I.41, D.48, M.49, F.52, I.84, P.85, L.91, I.154, Y.160 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.41, A:I.41 Hydrogen bonds: A:V.26, A:Y.160, A:T.178, A:T.178 Salt bridges: A:D.48 TMQ.12: 14 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, I.154, Y.160, T.178 Ligands: NAP.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.41, B:F.52, B:I.84 Hydrogen bonds: B:V.26, B:A.28, B:Y.160, B:T.178, B:T.178 Salt bridges: B:D.48

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

SO4.3: 4 residues within 4Å: Chain A: R.383, R.384 Chain B: R.423, S.424 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.424 Salt bridges: B:R.423, A:R.383, A:R.384 SO4.4: 3 residues within 4Å: Chain A: R.39, R.78, K.79 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.39, A:R.78, A:K.79 SO4.5: 2 residues within 4Å: Chain A: R.249, E.250 No protein-ligand interaction detected (PLIP) SO4.6: 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, A:E.336 Salt bridges: A:R.323 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 SO4.8: 3 residues within 4Å: Chain A: E.205, R.233, R.235 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.233, A:R.235 SO4.13: 5 residues within 4Å: Chain A: R.257, R.423, S.424 Chain B: R.383, R.384 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.383, B:R.384, A:R.423 Hydrogen bonds: A:S.424 SO4.14: 3 residues within 4Å: Chain B: R.60, R.286, Y.509 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.149, B:R.286, B:Y.509 Salt bridges: B:R.60 SO4.15: 2 residues within 4Å: Chain B: F.288, R.290 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.290 SO4.16: 4 residues within 4Å: Chain B: R.482, P.511, Y.512, P.513 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.482 SO4.17: 2 residues within 4Å: Chain B: R.491, R.493 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.493 Salt bridges: B:R.491 SO4.18: 3 residues within 4Å: Chain B: R.323, E.335, E.336 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.336, B:E.336 Salt bridges: B:R.323 SO4.19: 2 residues within 4Å: Chain B: R.78, K.79 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.78, B:K.79 SO4.20: 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

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

EDO.9: 4 residues within 4Å: Chain A: E.195, W.206, R.208, L.230 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: I.211, S.212, E.214, Y.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.212, A:E.214 EDO.21: 5 residues within 4Å: Chain B: I.211, S.212, E.213, E.214, Y.226 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.212, B:E.214 Water bridges: B:E.214, B:E.214 EDO.22: 4 residues within 4Å: Chain B: R.249, E.250, G.251 Ligands: EDO.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.249 EDO.23: 4 residues within 4Å: Chain A: N.413 Chain B: N.252, V.253 Ligands: EDO.22 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.413, A:N.413, B:V.253, B:V.253 EDO.24: 3 residues within 4Å: Chain B: H.255, G.261, S.467 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.467 EDO.25: 2 residues within 4Å: Chain B: W.206, R.208 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.206, B:R.208

Links

RCSB   PDBe   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
A

B
D

Dihydrofolate reductase-thymidylate synthase

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