SMTL ID : 1n2g.1

Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with AMPCPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.56, P.58, R.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.33 Water bridges: A:R.33 Salt bridges: A:R.56, A:R.154 SO4.9: 4 residues within 4Å: Chain B: R.56, V.57, P.58, R.154 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.56, B:R.154

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.161, R.198 Ligands: APC.3 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: K.160, D.161 Ligands: APC.11 No protein-ligand interaction detected (PLIP)

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

APC.3: 22 residues within 4Å: Chain A: P.38, T.39, 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.2, GOL.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:M.40, 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:V.187, A:M.195, A:S.197, A:R.198 Salt bridges: A:K.160, A:R.198 APC.11: 21 residues within 4Å: Chain B: P.38, 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.10, GOL.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:M.40, B:Y.82, B:G.158, B:K.160, B:D.161, B:D.161, B:Q.164, B:V.187, B:M.195, B:M.195, B:S.197, B:R.198 Water bridges: B:S.197, B:S.197, B:R.198 Salt bridges: B:K.160, B:R.198

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:D.174 Hydrogen bonds: A:Y.110, A:D.112, A:R.115, A:K.145 GOL.5: 7 residues within 4Å: Chain A: M.40, Q.72, V.139, V.142, V.143, Q.164 Ligands: APC.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.72, A:Q.164 GOL.6: 5 residues within 4Å: Chain A: L.114, R.115, T.117 Chain B: Q.119, P.120 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.119 Hydrogen bonds: A:R.115 GOL.12: 5 residues within 4Å: Chain B: Q.72, V.139, V.142, Q.164 Ligands: APC.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.72, B:Q.72, B:Q.164 GOL.13: 3 residues within 4Å: Chain A: Q.148, I.149 Chain B: N.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.176, B:N.176

4 x EOH: ETHANOL(Non-functional Binders)

EOH.7: 4 residues within 4Å: Chain A: V.166, R.169, I.255, G.256 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.170 EOH.8: 4 residues within 4Å: Chain A: E.189, L.193, N.199, R.207 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.199 Hydrogen bonds: A:E.189, A:N.199 EOH.14: 2 residues within 4Å: Chain B: H.222, T.225 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.225 EOH.15: 2 residues within 4Å: Chain B: R.169, A.173 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.169 Water bridges: B:A.173

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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