SMTL ID : 3imc.1 (1 other biounit)

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.6 Ang resolution in complex with fragment compound 5-methoxyindole, sulfate and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x BZ3: 5-methoxy-1H-indole(Non-covalent)

BZ3.1: 13 residues within 4Å: Chain A: H.45, G.47, H.48, A.50, L.51, G.159, K.161, V.185, P.186, T.187, V.188, M.196 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.51, A:K.161 Hydrogen bonds: A:V.188 Water bridges: A:K.161 pi-Cation interactions: A:H.45 BZ3.9: 12 residues within 4Å: Chain B: H.45, G.47, H.48, L.51, G.159, K.161, V.185, P.186, T.187, V.188, M.196 Ligands: SO4.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.161, B:T.187 Hydrogen bonds: B:V.188 Water bridges: B:G.159 pi-Stacking: B:H.45

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

SO4.2: 9 residues within 4Å: Chain A: H.45, H.48, K.161, D.162, M.196, S.197, S.198, R.199 Ligands: BZ3.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.83, A:D.162, A:S.198 Water bridges: A:K.161, A:S.198, A:S.198 Salt bridges: A:H.45, A:H.48, A:K.161, A:R.199 SO4.3: 4 residues within 4Å: Chain A: R.57, V.58, P.59, R.155 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.34, A:R.34 Salt bridges: A:R.57, A:R.155 SO4.10: 6 residues within 4Å: Chain B: H.45, K.161, M.196, S.197, S.198 Ligands: BZ3.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.198, B:S.198 Water bridges: B:S.198 Salt bridges: B:H.45, B:K.161 SO4.11: 1 residues within 4Å: Chain B: R.201 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.201 Salt bridges: B:R.201

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: M.41, Q.73, V.140, V.143, V.144, Q.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.73, A:Q.165 Water bridges: A:H.136, A:Q.165 GOL.5: 10 residues within 4Å: Chain A: M.110, Y.111, P.112, D.113, G.114, L.115, R.116, T.117, K.146 Chain B: D.175 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.110, A:D.113, A:R.116, A:T.117, A:K.146 Water bridges: B:D.175, B:N.177 GOL.12: 6 residues within 4Å: Chain B: P.39, M.41, Q.73, V.143, V.144, Q.165 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.39, B:Q.73, B:Q.73 Water bridges: B:M.41, B:Q.165

3 x EOH: ETHANOL(Non-functional Binders)

EOH.6: 5 residues within 4Å: Chain A: L.115, R.116, T.118 Chain B: Q.120, P.121 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.118, B:Q.120 Hydrogen bonds: A:L.115 EOH.7: 2 residues within 4Å: Chain A: P.112, D.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.113 EOH.8: 3 residues within 4Å: Chain A: M.72, Y.111, L.115 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.111, A:L.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hung, A.W. et al., Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase. Angew.Chem.Int.Ed.Engl. (2009)

Release Date

2009-10-13

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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