SMTL ID : 9kz4.1 (1 other biounit)

Dihydrofolate reductase binding to NADPH and trimethoprim-tetramethylrhodamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 28 residues within 4Å: Chain A: A.6, A.7, I.14, G.15, M.16, N.18, A.19, M.20, W.22, G.43, R.44, H.45, T.46, L.62, S.63, S.64, K.76, S.77, I.94, G.95, G.96, G.97, R.98, V.99, Y.100, Q.102, T.123 Ligands: 01.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:T.46 Hydrogen bonds: A:A.7, A:M.16, A:N.18, A:N.18, A:A.19, A:G.43, A:G.43, A:R.44, A:H.45, A:H.45, A:T.46, A:T.46, A:S.49, A:S.63, A:S.64, A:G.96, A:G.97, A:R.98, A:V.99, A:Y.100, A:Q.102 Water bridges: A:N.18, A:R.44, A:S.64, A:T.123, A:T.123 Salt bridges: A:R.44, A:H.45, A:H.45

1 x 01: [9-[5-[2-[4-[[2,4-bis(azanyl)pyrimidin-5-yl]methyl]-2,6-dimethoxy-phenoxy]ethylcarbamoyl]-2-carboxy-phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium

01.2: 15 residues within 4Å: Chain A: I.5, A.6, A.7, M.20, N.23, D.27, L.28, F.31, S.49, I.50, I.94, Y.100, T.113 Ligands: NDP.1, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.28, A:F.31, A:F.31 Hydrogen bonds: A:A.6, A:N.23, A:S.49, A:I.94, A:Y.100, A:T.113 Water bridges: A:M.20 Salt bridges: A:D.27

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 7 residues within 4Å: Chain A: I.5, A.6, W.30, Y.111, L.112, T.113 Ligands: 01.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.6, A:T.113 MG.4: 1 residues within 4Å: Chain A: E.120 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.120, H2O.1, H2O.3 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, K.C. et al., Dihydrofolate reductase binding to NADPH and trimethoprim-tetramethylrhodamine. To Be Published

Release Date

2025-01-22

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dihydrofolate reductase

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