SMTL ID : 4g5y.2 (1 other biounit)

Crystal Structure of Mycobacterium tuberculosis Pantothenate synthetase in a ternary complex with ATP and N,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: P.39, T.40, M.41, H.45, G.47, H.48, L.51, F.158, G.159, K.161, D.162, P.186, T.187, V.188, M.196, S.197, S.198, R.199 Ligands: MG.2, 0OC.3, GOL.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:M.41, A:G.159, A:K.161, A:D.162, A:D.162, A:Q.165, A:V.188, A:V.188, A:M.196, A:S.198, A:R.199 Water bridges: A:S.198, A:S.198, A:R.199, A:R.199 Salt bridges: A:H.45, A:H.48, A:H.48, A:K.161, A:K.161, A:R.199 ATP.8: 22 residues within 4Å: Chain B: P.39, T.40, M.41, G.42, H.45, G.47, H.48, L.51, Y.83, F.158, G.159, K.161, D.162, Q.165, P.186, T.187, V.188, M.196, S.197, S.198, R.199 Ligands: MG.9 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:M.41, B:Y.83, B:Y.83, B:G.159, B:K.161, B:D.162, B:D.162, B:Q.165, B:V.188, B:M.196, B:M.196, B:S.197, B:S.198, B:R.199 Water bridges: B:S.198, B:S.198, B:R.199 Salt bridges: B:H.45, B:H.48, B:H.48, B:K.161, B:K.161, B:R.199

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.162 Ligands: ATP.1, GOL.5 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: D.162 Ligands: ATP.8 No protein-ligand interaction detected (PLIP)

3 x 0OC: N,N-dimethylthiophene-3-sulfonamide(Non-covalent)(Covalent)

0OC.3: 12 residues within 4Å: Chain A: P.39, T.40, M.41, F.68, N.70, V.140, V.143, V.144, L.147, F.158, Q.165 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.143 Water bridges: A:T.40, A:Q.165 0OC.4: 9 residues within 4Å: Chain A: A.209, A.210, V.212, A.213, V.239, A.242, A.243, P.244 Chain B: A.227 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.212 Water bridges: A:A.210 0OC.10: 11 residues within 4Å: Chain B: P.39, T.40, M.41, F.68, N.70, Q.73, V.143, V.144, L.147, F.158, Q.165 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.143 Water bridges: B:T.40, B:Q.165, B:Q.165

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: K.161, D.162, S.197, S.198, R.199, R.279, L.281 Ligands: ATP.1, MG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.198, A:R.199, A:L.281 Water bridges: A:K.161, A:K.161 GOL.11: 9 residues within 4Å: Chain B: M.110, Y.111, P.112, D.113, G.114, L.115, R.116, T.117, K.146 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.111, B:D.113, B:R.116, B:K.146, B:K.146

4 x EOH: ETHANOL(Non-functional Binders)

EOH.6: 5 residues within 4Å: Chain A: G.245, A.247, R.274, L.275, G.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.245, A:G.276 Water bridges: A:Q.207 EOH.7: 1 residues within 4Å: Chain A: R.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.113, A:R.116, A:R.116 EOH.12: 3 residues within 4Å: Chain B: L.115, R.116, T.118 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.118 EOH.13: 4 residues within 4Å: Chain A: H.223, T.226 Chain B: A.216, T.219 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.226 Hydrogen bonds: B:T.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvestre, H.L. et al., Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-07-03

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Pantothenate synthetase

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