SMTL ID : 1n2b.1

Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with AMPCPP and pantoate, higher occupancy of pantoate and lower occupancy of AMPCPP in subunit A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.161 Ligands: APC.3 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: R.198 Ligands: APC.8 No protein-ligand interaction detected (PLIP)

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

SO4.2: 3 residues within 4Å: Chain A: R.56, P.58, R.154 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.56, A:R.154

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.3: 21 residues within 4Å: Chain A: P.38, M.40, G.41, H.44, G.46, H.47, L.50, Y.82, F.157, G.158, K.160, D.161, P.185, T.186, V.187, M.195, S.196, S.197, R.198 Ligands: MG.1, PAF.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:M.40, A:Y.82, A:Y.82, A:G.158, A:K.160, A:K.160, A:D.161, A:D.161, A:Q.164, A:V.187, A:M.195, A:M.195, A:S.197, A:R.198 Water bridges: A:P.38, A:R.198, A:R.198 Salt bridges: A:K.160, A:R.198 APC.8: 20 residues within 4Å: Chain B: M.40, H.44, G.46, H.47, L.50, Y.82, F.157, G.158, K.160, D.161, Q.164, P.185, T.186, V.187, M.195, S.196, S.197, R.198 Ligands: MG.7, GOL.10 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:M.40, B:G.158, B:K.160, B:D.161, B:Q.164, B:V.187, B:M.195, B:M.195, B:S.197, B:R.198 Water bridges: B:Y.82, B:Y.82, B:Y.82, B:S.196, B:R.198, B:R.198 Salt bridges: B:K.160, B:R.198

1 x PAF: PANTOATE(Non-covalent)

PAF.4: 11 residues within 4Å: Chain A: P.38, T.39, M.40, N.69, Q.72, V.139, V.142, V.143, F.157, Q.164 Ligands: APC.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.38, A:V.143, A:F.157 Hydrogen bonds: A:M.40, A:Q.72, A:Q.72, A:Q.164

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.110, A:D.112, A:R.115, A:K.145 Water bridges: B:N.176 GOL.9: 10 residues within 4Å: Chain A: D.174 Chain B: M.109, Y.110, P.111, D.112, G.113, L.114, R.115, T.116, K.145 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.174, B:Y.110, B:D.112, B:R.115, B:K.145 Water bridges: B:D.112 GOL.10: 6 residues within 4Å: Chain B: Q.72, V.139, V.142, V.143, Q.164 Ligands: APC.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.72, B:Q.164

5 x EOH: ETHANOL(Non-functional Binders)

EOH.6: 4 residues within 4Å: Chain A: M.40, Q.72, F.73, H.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.72 EOH.11: 5 residues within 4Å: Chain B: E.126, R.253, L.257, G.258, P.259 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.259 EOH.12: 6 residues within 4Å: Chain B: S.24, R.25, R.28, V.34, V.150, R.151 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.28 Hydrogen bonds: B:S.24 EOH.13: 2 residues within 4Å: Chain B: H.222, T.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.222 EOH.14: 6 residues within 4Å: Chain B: L.147, Q.148, R.151, P.152, D.178, V.179 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate. Protein Sci. (2003)

Release Date

2003-04-22

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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