SMTL ID : 3ix9.1 (2 other biounits)

Crystal structure of Streptococcus pneumoniae dihydrofolate reductase - Sp9 mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 26 residues within 4Å: Chain A: W.29, A.30, I.37, G.38, K.39, N.41, R.42, L.43, W.45, G.66, R.67, V.68, T.69, L.86, T.87, R.88, N.89, H.101, D.102, V.120, G.121, G.122, K.123, Q.124, I.125 Ligands: MTX.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:L.43 Hydrogen bonds: A:A.30, A:I.37, A:K.39, A:N.41, A:N.41, A:G.66, A:R.67, A:R.67, A:V.68, A:T.69, A:T.87, A:T.87, A:R.88, A:R.88, A:R.88, A:N.89, A:G.121, A:K.123, A:Q.124, A:Q.124, A:Q.124, A:I.125 Water bridges: A:R.88, A:V.103, A:T.149, A:T.149 Salt bridges: A:R.67 pi-Cation interactions: A:R.88, A:R.88 NDP.3: 26 residues within 4Å: Chain B: W.29, A.30, I.37, G.38, K.39, N.41, R.42, L.43, W.45, G.66, R.67, V.68, T.69, L.86, T.87, R.88, N.89, H.101, D.102, V.120, G.121, G.122, K.123, Q.124, I.125 Ligands: MTX.4 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:T.69 Hydrogen bonds: B:A.30, B:I.37, B:K.39, B:N.41, B:G.66, B:R.67, B:V.68, B:T.69, B:T.87, B:T.87, B:R.88, B:R.88, B:R.88, B:N.89, B:G.121, B:K.123, B:Q.124, B:Q.124, B:Q.124, B:I.125 Water bridges: B:N.41, B:V.103, B:T.149 Salt bridges: B:R.67 pi-Cation interactions: B:R.88, B:R.88

2 x MTX: METHOTREXATE(Non-covalent)

MTX.2: 15 residues within 4Å: Chain A: I.28, W.29, A.30, L.43, E.50, L.51, Q.52, F.54, K.55, L.78, R.81, V.120, T.139 Chain B: D.40 Ligands: NDP.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.54 Hydrogen bonds: A:I.28, A:T.139, A:T.139, B:D.40 Water bridges: A:W.29, A:E.50, A:E.50, A:Q.52, A:Q.52 Salt bridges: A:E.50, A:K.55, A:R.81 MTX.4: 17 residues within 4Å: Chain A: R.42 Chain B: I.28, W.29, A.30, L.43, P.48, E.50, L.51, Q.52, F.54, K.55, R.76, L.78, R.81, V.120, T.139 Ligands: NDP.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.51, B:L.51, B:F.54, B:K.55 Hydrogen bonds: B:I.28, B:R.76, B:T.139, B:T.139 Water bridges: B:E.50, B:E.50 Salt bridges: B:E.50, B:R.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J. et al., Kinetic and structural characterization of dihydrofolate reductase from Streptococcus pneumoniae. Biochemistry (2010)

Release Date

2010-02-02

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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