SMTL ID : 6vs8.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with ethyl 2-methyl thiazole-4-carboxylate(fragment 3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: H.159 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.40, B:H.159, H2O.1, H2O.2, H2O.3, H2O.4 CO.6: 3 residues within 4Å: Chain B: I.36, H.40, E.92 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.40, H2O.2, H2O.8, H2O.9, H2O.9, H2O.11

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 27 residues within 4Å: Chain A: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, W.24, G.45, R.46, R.47, T.48, L.67, S.68, R.69, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: RJY.4 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48 Hydrogen bonds: A:A.9, A:R.18, A:G.20, A:G.20, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:T.48, A:S.68, A:R.69, A:R.69, A:Q.70, A:G.98, A:G.99, A:Q.100, A:V.101, A:Y.102 Water bridges: A:G.17, A:S.68, A:R.69, A:R.69, A:Y.102 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NAP.7: 29 residues within 4Å: Chain B: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, G.45, R.46, R.47, T.48, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: PO4.9, RJY.10, SO4.13 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, B:R.18, B:G.20, B:G.20, B:G.45, B:G.45, B:R.46, B:R.46, B:R.47, B:R.47, B:R.47, B:T.48, B:T.48, B:S.68, B:R.69, B:R.69, B:Q.70, B:Q.70, B:G.98, B:G.99, B:Q.100, B:V.101, B:Y.102 Water bridges: B:R.47, B:S.51, B:R.69, B:R.69 Salt bridges: B:R.46, B:R.47 pi-Cation interactions: B:R.69

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: R.46, R.47 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.46, A:R.47 PO4.8: 6 residues within 4Å: Chain B: Q.30, F.33, R.34, L.59, R.62 Ligands: RJY.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.62 PO4.9: 3 residues within 4Å: Chain B: R.46, R.47 Ligands: NAP.7 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.46 Salt bridges: B:R.46, B:R.47

2 x RJY: ethyl 2-methyl-1,3-thiazole-4-carboxylate(Non-covalent)

RJY.4: 6 residues within 4Å: Chain A: D.29, Q.30, F.33, T.48, L.52 Ligands: NAP.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.48 Hydrogen bonds: A:Q.30 RJY.10: 7 residues within 4Å: Chain B: D.29, Q.30, F.33, L.52, I.96 Ligands: NAP.7, PO4.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.30 pi-Stacking: B:F.33

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

SO4.5: 1 residues within 4Å: Chain A: R.69 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.69 SO4.11: 3 residues within 4Å: Chain B: E.28, A.31, R.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.28 Salt bridges: B:R.148 SO4.12: 2 residues within 4Å: Chain B: R.34, P.60 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.34, B:R.62 Salt bridges: B:R.34 SO4.13: 2 residues within 4Å: Chain B: R.69 Ligands: NAP.7 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.69, B:R.69 Salt bridges: B:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.A. et al., Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis. Acs Infect Dis. (2020)

Release Date

2020-07-15

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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