SMTL ID : 5t7o.2 (1 other biounit)

Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase in complex with (6S)-5,6,7,8-TETRAHYDROFOLATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)

THG.1: 17 residues within 4Å: Chain A: V.26, V.27, A.28, D.48, M.49, F.52, R.53, T.80, P.85, F.88, L.91, P.92, R.94, I.154, Y.160, T.178 Ligands: NAP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.52, A:F.52, A:F.88 Hydrogen bonds: A:V.26, A:Y.160, A:T.178, A:T.178 Water bridges: A:R.53 Salt bridges: A:D.48, A:R.53, A:R.94 pi-Stacking: A:F.52 THG.17: 16 residues within 4Å: Chain B: V.26, V.27, A.28, D.48, M.49, F.52, R.53, I.84, F.88, L.91, P.92, R.94, I.154, Y.160, T.178 Ligands: NAP.15 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.88, B:L.91 Hydrogen bonds: B:V.26, B:Y.160, B:T.178, B:T.178 Water bridges: B:R.53, B:R.53 Salt bridges: B:D.48, B:R.53, B:R.94 pi-Stacking: B:F.52, B:F.52

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

NAP.2: 22 residues within 4Å: Chain A: V.27, A.28, I.35, G.36, G.77, R.78, K.79, T.80, S.83, L.99, S.100, S.101, T.102, G.130, G.131, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: THG.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.28, A:I.35, A:G.77, A:R.78, A:K.79, A:T.80, A:S.83, A:S.83, A:S.101, A:T.102, A:G.156, A:G.157, A:S.158, A:S.158, A:V.159, A:Y.160 Water bridges: A:K.79, A:T.80, A:S.101, A:E.162 Salt bridges: A:R.78 NAP.15: 22 residues within 4Å: Chain B: V.27, A.28, I.35, G.36, G.77, R.78, K.79, T.80, S.83, L.99, S.100, S.101, T.102, G.130, G.131, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: THG.17 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.35, B:I.35, B:Y.160 Hydrogen bonds: B:A.28, B:I.35, B:G.77, B:R.78, B:K.79, B:T.80, B:T.80, B:S.83, B:S.83, 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 UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.3: 12 residues within 4Å: Chain A: C.403, H.404, Q.422, R.423, S.424, D.426, G.430, N.434, H.464, Y.466 Chain B: R.383, R.384 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.422, A:S.424, A:S.424, A:D.426, A:N.434, A:N.434, A:H.464 Salt bridges: A:R.423, B:R.383, B:R.384 UMP.16: 15 residues within 4Å: Chain A: R.383, R.384 Chain B: C.403, H.404, Q.422, R.423, S.424, C.425, D.426, G.430, N.434, H.464, Y.466 Ligands: EDO.21, EDO.25 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.343, B:H.404, B:Q.422, B:S.424, B:D.426, B:N.434, B:N.434, B:H.464, B:Y.466 Salt bridges: B:R.423, A:R.383, A:R.384

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

EDO.4: 7 residues within 4Å: Chain A: A.174, Y.176, K.229, I.231, R.482, A.510 Ligands: EDO.11 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: H.255, S.467 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: F.4, R.348, H.349, E.497 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: I.248, R.249, V.470, N.474 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: R.271, Y.410, S.412, S.417, E.455 Chain B: N.252 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: A.140, S.141, P.142, T.145, F.489, R.490 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: P.166, P.167 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: S.24, T.150, Y.152, Y.176 Ligands: EDO.4 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: A.371, I.372, R.384, L.386 Chain B: W.390 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: T.332, E.333, Y.334, E.335 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: W.289, V.506, Y.509 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: A.174, Y.176, K.229, I.231, R.482, A.510 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: F.4, R.301, R.348, H.349, D.362, E.497 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: I.248, R.249, V.470, N.474 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: I.316, W.317, N.320 Ligands: UMP.16 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: G.302, T.304, F.345, H.357, D.358, Y.361 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: A.371, I.372, R.384, L.386 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain A: F.350, G.351, N.391, S.393 Chain B: F.350, G.351, N.391, S.393 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: G.430, F.433 Ligands: UMP.16 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain B: L.18, A.140, P.142, T.145, V.488, F.489, R.490 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: R.286, W.289, V.506, Y.509 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Pisa, F. et al., Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase in complex with (6S)-5,6,7,8-TETRAHYDROFOLATE. To Be Published

Release Date

2017-09-20

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Bifunctional dihydrofolate reductase-thymidylate synthase

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