SMTL ID : 3nrr.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: A.437, Q.441 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

NAP.2: 26 residues within 4Å: Chain A: V.19, A.20, I.27, G.28, H.29, N.31, Q.32, I.33, W.35, G.70, R.71, K.72, T.73, S.76, L.92, S.93, R.94, T.95, L.127, G.129, S.130, F.131, Y.133, E.135, T.158 Ligands: D16.3 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:A.20, A:I.27, A:H.29, A:N.31, A:G.70, A:G.70, A:R.71, A:R.71, A:K.72, A:T.73, A:S.76, A:S.76, A:R.94, A:R.94, A:R.94, A:T.95, A:G.129, A:S.130, A:F.131, A:L.132, A:E.135, A:E.135, A:T.158 Water bridges: A:N.31, A:R.94, A:S.130 Salt bridges: A:R.71 pi-Cation interactions: A:R.94 NAP.18: 29 residues within 4Å: Chain B: V.19, A.20, I.27, G.28, H.29, N.31, Q.32, I.33, W.35, G.70, R.71, K.72, T.73, S.76, L.92, S.93, R.94, T.95, E.106, D.107, L.127, G.129, S.130, F.131, L.132, Y.133, E.135, T.158 Ligands: D16.19 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:T.73 Hydrogen bonds: B:A.20, B:I.27, B:H.29, B:N.31, B:G.70, B:G.70, B:R.71, B:R.71, B:K.72, B:T.73, B:T.73, B:S.76, B:S.76, B:S.93, B:R.94, B:R.94, B:T.95, B:G.129, B:S.130, B:F.131, B:L.132, B:E.135, B:T.158 Water bridges: B:N.31, B:L.108 Salt bridges: B:R.71

4 x D16: TOMUDEX(Non-covalent)

D16.3: 14 residues within 4Å: Chain A: F.18, V.19, A.20, D.41, F.42, L.45, R.46, T.73, I.77, P.78, S.81, L.127, T.148 Ligands: NAP.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.42, A:I.77, A:L.127 Hydrogen bonds: A:F.18, A:D.41, A:S.81 Water bridges: A:R.46, A:R.87 Salt bridges: A:R.46 D16.5: 14 residues within 4Å: Chain A: A.282, S.285, E.289, I.310, W.311, N.314, D.420, L.423, G.424, F.427, Y.460, M.513, S.514 Ligands: UMP.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.282, A:W.311, A:F.427, A:F.427, A:Y.460 Hydrogen bonds: A:S.285, A:D.420, A:G.424 Water bridges: A:K.279, A:I.509, A:S.514, A:S.514, A:A.515 Salt bridges: A:K.279 D16.19: 16 residues within 4Å: Chain B: F.18, V.19, A.20, H.37, D.41, F.42, L.45, R.46, F.69, T.73, I.77, P.78, S.81, L.127, T.148 Ligands: NAP.18 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.42, B:F.42, B:L.45, B:I.77, B:L.127 Hydrogen bonds: B:F.18, B:R.46, B:S.81 Salt bridges: B:H.37 D16.21: 15 residues within 4Å: Chain B: A.282, S.285, E.289, I.310, W.311, N.314, D.420, L.423, G.424, F.427, Y.460, M.513, S.514, A.515 Ligands: UMP.20 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.282, B:W.311, B:F.427, B:F.427, B:Y.460 Hydrogen bonds: B:S.285, B:D.420, B:G.424, B:A.515 Water bridges: B:S.514 Salt bridges: B:K.279

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

UMP.4: 17 residues within 4Å: Chain A: R.252, Y.337, L.394, C.397, H.398, Q.416, R.417, S.418, C.419, D.420, G.424, N.428, H.458, Y.460 Chain B: R.377, R.378 Ligands: D16.5 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:D.420 Hydrogen bonds: A:Q.416, A:S.418, A:D.420, A:N.428, A:N.428, A:H.458, A:Y.460 Salt bridges: A:R.252, A:R.417, B:R.377, B:R.378 Water bridges: B:R.377 UMP.20: 17 residues within 4Å: Chain A: R.377, R.378 Chain B: R.252, Y.337, L.394, C.397, H.398, Q.416, R.417, S.418, C.419, D.420, G.424, N.428, H.458, Y.460 Ligands: D16.21 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.416, B:S.418, B:S.418, B:D.420, B:N.428, B:N.428, B:H.458, B:Y.460 Water bridges: B:R.252, A:R.377 Salt bridges: B:R.252, B:R.417, A:R.377, A:R.378

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

EDO.6: 9 residues within 4Å: Chain A: I.360, Q.362, E.365, I.366, I.380 Chain B: W.384, V.386, L.389 Ligands: EDO.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.384, A:E.365 EDO.7: 3 residues within 4Å: Chain A: K.218, Y.219, V.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.220 EDO.8: 7 residues within 4Å: Chain A: I.360, E.365, R.369 Chain B: V.386, L.389, K.390 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.369 Water bridges: A:E.365, A:R.369 EDO.9: 3 residues within 4Å: Chain A: F.167, Y.188, K.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.191, A:K.191 Water bridges: A:P.164 EDO.10: 5 residues within 4Å: Chain A: V.21, K.25, F.160, P.161, D.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162 Water bridges: A:I.163, A:Y.188, A:Y.188 EDO.11: 3 residues within 4Å: Chain A: Y.219, L.243, Y.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.219 Water bridges: A:L.243, A:S.244 EDO.12: 6 residues within 4Å: Chain A: R.43, F.44, N.47 Chain B: L.206, G.209, T.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.43, A:N.47 EDO.14: 5 residues within 4Å: Chain A: D.203 Chain B: T.170, I.187, E.189, I.227 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.144, B:T.170, A:D.203 Water bridges: B:E.189 EDO.15: 5 residues within 4Å: Chain A: T.170, E.189, R.226, I.227 Chain B: D.203 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.170, B:D.203, B:D.203 Water bridges: A:E.189 EDO.22: 7 residues within 4Å: Chain A: W.384, V.386, L.389 Chain B: Q.362, E.365, I.366, I.380 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.365, A:W.384 Water bridges: B:R.369 EDO.23: 5 residues within 4Å: Chain B: K.218, Y.219, L.243, Y.258, V.464 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.218, B:L.243 EDO.24: 5 residues within 4Å: Chain B: I.163, P.164, D.165, F.167, Y.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.167 Water bridges: B:I.169 EDO.25: 3 residues within 4Å: Chain B: T.110, R.113, D.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.113, B:D.114

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: Q.441, P.485, R.488 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.488 Water bridges: A:Q.441, A:Q.441, A:R.488

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 5 residues within 4Å: Chain B: N.24, V.26, P.155, G.156, Y.159 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.24, B:G.156, B:G.156, B:Y.159, B:Y.159

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

2010-07-14

Peptides

Dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase-thymidylate synthase