SMTL ID : 6nne.2 (2 other biounits)

Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with diaverdine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x CO: COBALT (II) ION(Non-covalent)

CO.1: 3 residues within 4Å: Chain A: I.34, H.38, E.90 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.38, H2O.1, H2O.2, H2O.3, H2O.3

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

NDP.2: 27 residues within 4Å: Chain A: W.6, A.7, I.14, G.15, R.16, G.18, D.19, I.20, G.43, R.44, R.45, T.46, L.65, S.66, R.67, Q.68, G.80, I.94, G.95, G.96, G.97, Q.98, V.99, Y.100, L.102, A.126 Ligands: KUP.3 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:I.20, A:T.46 Hydrogen bonds: A:A.7, A:I.14, A:R.16, A:G.18, A:G.18, A:G.43, A:R.44, A:R.44, A:R.45, A:R.45, A:T.46, A:T.46, A:S.66, A:R.67, A:R.67, A:R.67, A:Q.68, A:Q.68, A:G.96, A:G.97, A:Q.98, A:V.99 Water bridges: A:R.16, A:S.49, A:L.82 Salt bridges: A:R.44, A:R.45 pi-Cation interactions: A:R.67, A:R.67

1 x KUP: 5-[(3,4-dimethoxyphenyl)methyl]pyrimidine-2,4-diamine(Non-covalent)

KUP.3: 13 residues within 4Å: Chain A: I.5, W.6, A.7, I.20, D.27, Q.28, F.31, S.49, L.50, L.57, I.94, Y.100 Ligands: NDP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.20, A:F.31, A:F.31, A:L.50 Hydrogen bonds: A:I.5, A:W.6, A:A.7, A:Q.28, A:Y.100 Water bridges: A:T.113 Salt bridges: A:D.27 pi-Stacking: A:F.31

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

SO4.4: 2 residues within 4Å: Chain A: E.26, A.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.146 Water bridges: A:H.30 SO4.5: 2 residues within 4Å: Chain A: R.44, R.45 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.44 Salt bridges: A:R.44, A:R.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.A. et al., Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-07-17

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dihydrofolate reductase

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