SMTL ID : 3k2h.1

Co-crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis with dUMP, Pemetrexed and NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 17 residues within 4Å: Chain A: R.248, Y.333, L.390, C.393, H.394, Q.412, R.413, S.414, C.415, D.416, G.420, N.424, H.454, Y.456 Chain B: R.373, R.374 Ligands: LYA.2 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.412, A:S.414, A:D.416, A:N.424, A:N.424, A:H.454, A:Y.456 Salt bridges: A:R.248, A:R.413, B:R.373, B:R.374 Water bridges: B:R.373 UMP.8: 17 residues within 4Å: Chain A: R.373, R.374 Chain B: R.248, Y.333, L.390, C.393, H.394, Q.412, R.413, S.414, C.415, D.416, G.420, N.424, H.454, Y.456 Ligands: LYA.9 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.412, B:S.414, B:D.416, B:N.424, B:N.424, B:H.454 Salt bridges: B:R.248, B:R.413, A:R.373, A:R.374 Water bridges: A:R.373

4 x LYA: 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID(Non-covalent)

LYA.2: 15 residues within 4Å: Chain A: A.278, S.281, E.285, I.306, W.307, N.310, L.390, D.416, L.419, G.420, F.423, Y.456, M.509, S.510 Ligands: UMP.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:A.278, A:I.306, A:I.306, A:F.423, A:F.423, A:F.423 Hydrogen bonds: A:S.281, A:N.310, A:Y.456, A:S.510, A:S.510, A:S.510 Water bridges: A:S.281, A:I.306, A:N.310, A:I.505, A:M.507, A:M.509 Salt bridges: A:K.275, A:D.416 pi-Stacking: A:W.307 LYA.3: 17 residues within 4Å: Chain A: F.14, V.15, A.16, D.37, F.38, R.39, L.41, R.42, T.69, I.73, S.77, L.80, R.83, L.123, Y.129, T.144 Ligands: NAP.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.38, A:F.38, A:L.41, A:T.69, A:I.73, A:I.73, A:L.80 Hydrogen bonds: A:F.14, A:F.14, A:S.77, A:T.144, A:T.144 Water bridges: A:S.77, A:K.81, A:T.144 Salt bridges: A:D.37, A:R.42, A:R.83 LYA.9: 15 residues within 4Å: Chain B: A.278, S.281, E.285, I.306, W.307, N.310, L.390, D.416, L.419, G.420, F.423, Y.456, M.509, S.510 Ligands: UMP.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.278, B:I.306, B:I.306 Hydrogen bonds: B:S.281, B:N.310, B:S.510, B:S.510, B:S.510 Water bridges: B:S.281, B:I.306, B:N.310, B:I.505, B:I.505, B:M.507, B:M.509 Salt bridges: B:K.275, B:D.416 pi-Stacking: B:W.307, B:F.423 LYA.10: 19 residues within 4Å: Chain B: F.14, V.15, A.16, I.29, D.37, F.38, R.39, L.41, R.42, T.69, S.72, I.73, S.77, L.80, R.83, L.123, Y.129, T.144 Ligands: NAP.11 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.29, B:F.38, B:F.38, B:L.41, B:T.69, B:I.73, B:I.73, B:L.80 Hydrogen bonds: B:F.14, B:F.14, B:D.37, B:S.77, B:T.144, B:T.144 Salt bridges: B:D.37, B:R.39, B:R.42, B:R.83

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

NAP.4: 30 residues within 4Å: Chain A: V.15, A.16, I.23, G.24, H.25, N.27, Q.28, I.29, W.31, G.66, R.67, K.68, T.69, S.72, L.88, S.89, R.90, T.91, E.102, D.103, L.104, L.123, G.124, G.125, S.126, F.127, Y.129, E.131, T.154 Ligands: LYA.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.23, A:T.69, A:Y.129 Hydrogen bonds: A:A.16, A:I.23, A:H.25, A:G.66, A:R.67, A:R.67, A:K.68, A:T.69, A:T.69, A:S.72, A:S.72, A:S.89, A:R.90, A:R.90, A:T.91, A:T.91, A:L.104, A:G.125, A:S.126, A:F.127, A:L.128, A:Y.129, A:E.131 Water bridges: A:N.27, A:T.154, A:T.154 Salt bridges: A:R.67 NAP.11: 30 residues within 4Å: Chain B: V.15, A.16, I.23, G.24, H.25, N.27, Q.28, I.29, W.31, G.66, R.67, K.68, T.69, S.72, L.88, S.89, R.90, T.91, E.102, D.103, L.104, L.123, G.124, G.125, S.126, F.127, Y.129, E.131, T.154 Ligands: LYA.10 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.23, B:T.69 Hydrogen bonds: B:A.16, B:I.23, B:H.25, B:N.27, B:G.66, B:R.67, B:K.68, B:T.69, B:S.72, B:S.72, B:R.90, B:R.90, B:R.90, B:T.91, B:T.91, B:L.104, B:G.124, B:G.125, B:S.126, B:F.127, B:L.128, B:E.131 Water bridges: B:T.154 Salt bridges: B:R.67

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

EDO.5: 7 residues within 4Å: Chain A: Q.358, E.361, I.362, I.376 Chain B: W.380, V.382, L.385 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.361, A:E.361, B:W.380 EDO.6: 8 residues within 4Å: Chain A: W.380, V.382, L.385 Chain B: I.356, Q.358, E.361, I.362, I.376 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.380, B:E.361 EDO.7: 6 residues within 4Å: Chain A: R.374 Chain B: R.248, N.319, A.389, L.390, P.391 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.389, A:R.374, A:R.374 EDO.12: 6 residues within 4Å: Chain A: R.248, N.319, A.389, L.390, P.391 Chain B: R.374 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.248, A:A.389, B:R.374, B:R.374 EDO.13: 8 residues within 4Å: Chain A: F.340, G.341, N.381, S.383 Chain B: F.340, G.341, N.381, S.383 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.383, B:S.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Begley, D.W. et al., Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis. Acta Crystallogr.,Sect.F (2011)

Release Date

2009-10-13

Peptides

Dihydrofolate reductase/thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase/thymidylate synthase

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