SMTL ID : 4ddh.1

Pantothenate synthetase in complex with 6-methoxy-1-benzofuran-3-yl acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

3 x EOH: ETHANOL(Non-functional Binders)

EOH.1: 6 residues within 4Å: Chain A: L.114, R.115, T.117 Chain B: Q.119, P.120, G.121 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.117, B:Q.119 EOH.2: 2 residues within 4Å: Chain A: A.215, T.218 No protein-ligand interaction detected (PLIP) EOH.9: 2 residues within 4Å: Chain B: G.288, T.289 No protein-ligand interaction detected (PLIP)

2 x MS0: (6-methoxy-1-benzofuran-3-yl)acetic acid(Non-covalent)

MS0.3: 11 residues within 4Å: Chain A: H.44, G.46, H.47, K.160, D.161, P.185, T.186, V.187, M.195, S.196, S.197 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.160 Hydrogen bonds: A:V.187, A:S.197 Salt bridges: A:H.44, A:H.47, A:K.160, A:R.198 pi-Stacking: A:H.44, A:H.44 MS0.7: 12 residues within 4Å: Chain B: H.44, G.46, H.47, L.50, K.160, D.161, P.185, T.186, V.187, M.195, S.196, S.197 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.160 Hydrogen bonds: B:V.187, B:S.197 Salt bridges: B:H.44, B:K.160 pi-Cation interactions: B:H.44, B:H.47

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 8 residues within 4Å: Chain A: M.109, Y.110, G.113, L.114, R.115, T.116, K.145 Chain B: D.174 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.109, A:R.115, A:T.116, A:K.145 Water bridges: A:D.112, B:N.176 EDO.5: 4 residues within 4Å: Chain A: P.38, T.39, M.40, Q.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.38, A:Q.72 Water bridges: A:Q.164 EDO.6: 3 residues within 4Å: Chain A: L.252, P.261, L.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.262 EDO.8: 9 residues within 4Å: Chain A: D.174 Chain B: M.109, Y.110, G.113, L.114, R.115, T.116, T.117, K.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.115, B:K.145, B:K.145 Water bridges: B:D.112 EDO.12: 4 residues within 4Å: Chain A: P.17, G.18, A.21 Chain B: N.176 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.176, A:P.17 Water bridges: B:A.173, B:L.177 EDO.13: 2 residues within 4Å: Chain B: P.4, D.19 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.19, B:D.19

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain B: G.244, A.246, R.273, L.274, G.275 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.244, B:G.275 Water bridges: B:Q.206, B:R.273 GOL.11: 1 residues within 4Å: Chain B: P.243 No protein-ligand interaction detected (PLIP)

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

2013-02-13

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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