SMTL ID : 3s3v.2 (1 other biounit)

human dihydrofolate reductase Q35K/N64F double mutant binary complex with trimethoprim

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-trimer

Ligands

6 x TOP: TRIMETHOPRIM(Non-covalent)

TOP.1: 15 residues within 4Å: Chain A: I.7, V.8, A.9, E.30, F.31, F.34, K.35, T.56, I.60, F.64, L.67, V.115, Y.121, T.136 Ligands: TOP.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.34 Hydrogen bonds: A:I.7, A:K.35, A:Y.121, A:T.136, A:T.136 Water bridges: A:A.9, A:R.70 Salt bridges: A:E.30 pi-Stacking: A:F.34 TOP.7: 12 residues within 4Å: Chain A: G.20, D.21, L.22, F.31, S.59, I.60, P.61, F.64 Chain C: K.63 Ligands: TOP.1, SO4.5, SO4.13 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.63 Hydrophobic interactions: A:L.22, A:F.31 TOP.8: 15 residues within 4Å: Chain B: I.7, V.8, A.9, E.30, F.31, F.34, K.35, T.56, I.60, F.64, L.67, V.115, Y.121, T.136 Ligands: TOP.14 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.34 Hydrogen bonds: B:I.7, B:K.35, B:Y.121, B:T.136, B:T.136 Water bridges: B:A.9, B:R.70 Salt bridges: B:E.30 pi-Stacking: B:F.34 TOP.14: 12 residues within 4Å: Chain A: K.63 Chain B: G.20, D.21, L.22, F.31, S.59, I.60, P.61, F.64 Ligands: TOP.8, SO4.12, SO4.20 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.63 Hydrophobic interactions: B:L.22, B:F.31 TOP.15: 15 residues within 4Å: Chain C: I.7, V.8, A.9, E.30, F.31, F.34, K.35, T.56, I.60, F.64, L.67, V.115, Y.121, T.136 Ligands: TOP.21 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.34 Hydrogen bonds: C:I.7, C:K.35, C:Y.121, C:T.136, C:T.136 Water bridges: C:A.9, C:R.70 Salt bridges: C:E.30 pi-Stacking: C:F.34 TOP.21: 12 residues within 4Å: Chain B: K.63 Chain C: G.20, D.21, L.22, F.31, S.59, I.60, P.61, F.64 Ligands: SO4.6, TOP.15, SO4.19 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.22, C:F.31 Hydrogen bonds: B:K.63

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

SO4.2: 6 residues within 4Å: Chain A: G.53, K.54, K.55, T.56, G.117, V.120 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.53, A:K.55, A:T.56, A:T.56, A:G.117 Water bridges: A:K.54, A:S.119 SO4.3: 4 residues within 4Å: Chain A: K.54, S.76, R.77, E.78 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.77, A:E.78, A:E.78, A:E.78 Water bridges: A:L.75 Salt bridges: A:K.54 SO4.4: 4 residues within 4Å: Chain A: V.165, L.166, S.167, D.168 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.167, A:D.168 Water bridges: A:V.165, A:S.167, A:S.167 SO4.5: 9 residues within 4Å: Chain A: K.63, F.64 Chain C: K.63 Ligands: SO4.6, TOP.7, SO4.12, SO4.13, SO4.19, SO4.20 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:K.63, A:K.63 SO4.6: 9 residues within 4Å: Chain A: K.63 Chain B: K.63 Chain C: K.63 Ligands: SO4.5, SO4.12, SO4.13, SO4.19, SO4.20, TOP.21 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Salt bridges: B:K.63, C:K.63, A:K.63 Water bridges: C:K.63 SO4.9: 6 residues within 4Å: Chain B: G.53, K.54, K.55, T.56, G.117, V.120 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.53, B:K.55, B:T.56, B:T.56, B:G.117 Water bridges: B:K.54, B:S.119 SO4.10: 4 residues within 4Å: Chain B: K.54, S.76, R.77, E.78 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.77, B:E.78, B:E.78, B:E.78 Water bridges: B:L.75 Salt bridges: B:K.54 SO4.11: 4 residues within 4Å: Chain B: V.165, L.166, S.167, D.168 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.167, B:D.168 Water bridges: B:V.165, B:S.167, B:S.167 SO4.12: 9 residues within 4Å: Chain A: K.63 Chain B: K.63, F.64 Ligands: SO4.5, SO4.6, SO4.13, TOP.14, SO4.19, SO4.20 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.63, A:K.63 SO4.13: 9 residues within 4Å: Chain A: K.63 Chain B: K.63 Chain C: K.63 Ligands: SO4.5, SO4.6, TOP.7, SO4.12, SO4.19, SO4.20 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Salt bridges: B:K.63, C:K.63, A:K.63 Water bridges: A:K.63 SO4.16: 6 residues within 4Å: Chain C: G.53, K.54, K.55, T.56, G.117, V.120 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.53, C:K.55, C:T.56, C:T.56, C:G.117 Water bridges: C:K.54, C:S.119 SO4.17: 4 residues within 4Å: Chain C: K.54, S.76, R.77, E.78 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.77, C:E.78, C:E.78, C:E.78 Water bridges: C:L.75 Salt bridges: C:K.54 SO4.18: 4 residues within 4Å: Chain C: V.165, L.166, S.167, D.168 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.167, C:D.168 Water bridges: C:V.165, C:S.167, C:S.167 SO4.19: 9 residues within 4Å: Chain B: K.63 Chain C: K.63, F.64 Ligands: SO4.5, SO4.6, SO4.12, SO4.13, SO4.20, TOP.21 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:K.63, C:K.63 SO4.20: 9 residues within 4Å: Chain A: K.63 Chain B: K.63 Chain C: K.63 Ligands: SO4.5, SO4.6, SO4.12, SO4.13, TOP.14, SO4.19 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Salt bridges: A:K.63, B:K.63, C:K.63 Water bridges: B:K.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cody, V. et al., Crystallographic analysis reveals a novel second binding site for trimethoprim in active site double mutants of human dihydrofolate reductase. J.Struct.Biol. (2011)

Release Date

2011-09-28

Peptides

Dihydrofolate reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Dihydrofolate reductase

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