SMTL ID : 8crh.1

Crystal structure of Candida auris dihydrofolate reductase complexed with NADPH and cycloguanil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x VIL: 5-(4-chlorophenyl)-6,6-dimethyl-1,4-dihydro-1,3,5-triazine-2,4-diamine(Non-covalent)

VIL.1: 14 residues within 4Å: Chain A: I.14, V.15, A.16, L.30, E.37, M.38, F.41, T.62, I.66, I.125, Y.131, T.146 Ligands: NDP.2, VIL.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.16, A:L.30, A:F.41 Hydrogen bonds: A:I.14, A:T.146, A:T.146 Water bridges: A:T.146 Salt bridges: A:E.37 pi-Stacking: A:F.41 VIL.3: 8 residues within 4Å: Chain A: L.30, L.65, P.67, F.70, L.73 Ligands: VIL.1, NDP.2, SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.30, A:L.65, A:L.73 VIL.5: 14 residues within 4Å: Chain B: I.14, V.15, A.16, L.30, E.37, M.38, F.41, T.62, I.66, I.125, Y.131, T.146 Ligands: NDP.6, VIL.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.16, B:L.30, B:I.125 Hydrogen bonds: B:I.14, B:T.146, B:T.146 Water bridges: B:T.146 Salt bridges: B:E.37 pi-Stacking: B:F.41 Halogen bonds: B:T.62 VIL.7: 6 residues within 4Å: Chain B: L.30, M.38, L.65, F.70 Ligands: VIL.5, SO4.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.30, B:F.70 pi-Cation interactions: B:F.70

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

NDP.2: 29 residues within 4Å: Chain A: V.15, A.16, I.24, G.25, A.26, G.28, S.29, L.30, G.59, R.60, K.61, T.62, L.65, L.81, S.82, R.83, K.84, S.98, I.125, G.126, G.127, S.128, Q.129, I.130, Y.131, L.133, T.162 Ligands: VIL.1, VIL.3 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:L.30, A:T.62, A:Y.131 Hydrogen bonds: A:A.16, A:I.24, A:A.26, A:G.28, A:S.29, A:G.59, A:R.60, A:R.60, A:K.61, A:T.62, A:T.62, A:S.82, A:R.83, A:R.83, A:R.83, A:G.126, A:G.127, A:S.128, A:Q.129, A:Q.129, A:Q.129, A:I.130, A:Y.131 Water bridges: A:R.83, A:K.84, A:T.162 Salt bridges: A:R.60, A:K.84 pi-Cation interactions: A:R.83 NDP.6: 25 residues within 4Å: Chain B: V.15, A.16, I.24, G.25, G.28, S.29, L.30, G.59, R.60, K.61, T.62, L.65, L.81, S.82, R.83, S.98, I.125, G.126, G.127, S.128, Q.129, I.130, Y.131, L.133 Ligands: VIL.5 32 PLIP interactions: 31 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.131 Hydrogen bonds: B:A.16, B:G.59, B:G.59, B:R.60, B:R.60, B:K.61, B:T.62, B:T.62, B:R.83, B:R.83, B:G.127, B:S.128, B:Q.129, B:Q.129, B:I.130, B:Y.131, B:Y.131 Water bridges: B:G.28, B:K.61, B:S.82, B:R.83, B:K.84, B:K.84, B:F.100, B:S.128, B:Q.129, B:T.162, A:Q.181 Salt bridges: B:R.60, B:K.61 pi-Cation interactions: B:R.83

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

SO4.4: 5 residues within 4Å: Chain A: K.42, F.70, L.73, R.76 Ligands: VIL.3 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.42, A:K.42, A:A.74, A:R.76, A:R.76 Salt bridges: A:K.42, A:R.76 SO4.8: 2 residues within 4Å: Chain B: R.60, K.61 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.60, B:R.60, B:K.61, B:K.61, B:K.61 Salt bridges: B:R.60, B:K.61 SO4.9: 2 residues within 4Å: Chain B: D.90, S.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.91 Water bridges: B:D.90 SO4.10: 5 residues within 4Å: Chain B: F.41, K.42, L.73, R.76 Ligands: VIL.7 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.42, B:A.74, B:R.76 Salt bridges: B:R.76 SO4.11: 1 residues within 4Å: Chain B: L.185 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirkman, T. et al., Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-08-02

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Dihydrofolate reductase