SMTL ID : 4g5f.1 (1 other biounit)

Pantothenate synthetase in complex with racemate (2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID and (2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: M.109, Y.110, P.111, D.112, G.113, L.114, R.115, T.116, K.145 Chain B: D.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.110, A:D.112, A:R.115, A:K.145

2 x 0JD: (2S)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid(Non-covalent)

0JD.2: 8 residues within 4Å: Chain A: P.38, T.39, M.40, H.47, V.143, F.157, Q.164 Ligands: 15N.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.38, A:V.143, A:F.157 Hydrogen bonds: A:M.40, A:Q.164 Salt bridges: A:H.47 0JD.10: 8 residues within 4Å: Chain B: P.38, T.39, M.40, H.47, V.143, F.157, Q.164 Ligands: 15N.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.38, B:V.143, B:F.157 Hydrogen bonds: B:M.40, B:Q.164 Water bridges: B:H.47 Salt bridges: B:H.47

2 x 15N: (2R)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid(Non-covalent)

15N.3: 8 residues within 4Å: Chain A: P.38, T.39, M.40, H.47, V.143, F.157, Q.164 Ligands: 0JD.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.38, A:V.143, A:F.157 Hydrogen bonds: A:M.40, A:Q.164 Salt bridges: A:H.47 15N.8: 8 residues within 4Å: Chain B: P.38, T.39, M.40, H.47, V.143, F.157, Q.164 Ligands: 0JD.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.38, B:V.143, B:F.157 Hydrogen bonds: B:M.40, B:Q.164 Water bridges: B:H.47 Salt bridges: B:H.47

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

EDO.4: 2 residues within 4Å: Chain A: P.111, D.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.112 EDO.5: 7 residues within 4Å: Chain A: L.114, R.115, T.117 Chain B: Q.119, P.120, G.121, P.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.117 EDO.11: 6 residues within 4Å: Chain B: Y.110, L.114, T.117, A.137, G.138, T.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.110, B:Y.110

3 x EOH: ETHANOL(Non-functional Binders)

EOH.6: 4 residues within 4Å: Chain A: P.70, M.71, Y.110, L.114 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.110, A:L.114 Hydrogen bonds: A:P.70 EOH.7: 5 residues within 4Å: Chain B: S.24, R.25, R.28, V.150, R.151 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.151 Hydrogen bonds: B:S.24 EOH.9: 1 residues within 4Å: Chain B: I.3 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

2013-07-17

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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