SMTL ID : 3iod.1

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.75 Ang resolution in complex with 5'-deoxy-5'-((3-nitrobenzyl)disulfanyl)-adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x A6D: (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-{[(3-nitrobenzyl)disulfanyl]methyl}tetrahydrofuran-3,4-diol(Non-covalent)

A6D.1: 24 residues within 4Å: Chain A: P.39, T.40, M.41, H.45, G.47, H.48, L.51, S.66, F.68, N.70, Q.73, V.140, V.143, L.147, F.158, G.159, K.161, D.162, Q.165, P.186, T.187, V.188, M.196 Ligands: SO4.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.70, A:V.140, A:V.143 Hydrogen bonds: A:G.159, A:D.162, A:D.162, A:V.188, A:V.188, A:M.196 Water bridges: A:T.40, A:Q.165, A:Q.165 A6D.7: 22 residues within 4Å: Chain B: P.39, T.40, M.41, H.45, G.47, H.48, L.51, F.68, N.70, V.140, V.143, L.147, F.158, G.159, K.161, D.162, Q.165, P.186, T.187, V.188, M.196 Ligands: SO4.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.70, B:V.140, B:V.143 Hydrogen bonds: B:G.159, B:K.161, B:D.162, B:D.162, B:V.188, B:V.188, B:M.196 Water bridges: B:Q.165, B:Q.165

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

SO4.2: 8 residues within 4Å: Chain A: H.45, H.48, Y.83, K.161, S.197, S.198, R.199 Ligands: A6D.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.83, A:S.197, A:S.198 Salt bridges: A:H.45, A:H.48, A:K.161, A:R.199 SO4.8: 6 residues within 4Å: Chain B: H.45, H.48, K.161, S.197, S.198 Ligands: A6D.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.198, B:S.198 Water bridges: B:K.161, B:K.161, B:K.161, B:S.198, B:S.198 Salt bridges: B:H.45, B:H.48, B:K.161

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.111, A:D.113, A:R.116, A:K.146, A:K.146 GOL.4: 2 residues within 4Å: Chain A: P.112, D.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.113

3 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 5 residues within 4Å: Chain A: L.115, R.116, T.118 Chain B: Q.120, P.121 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.120, A:T.118 EOH.6: 2 residues within 4Å: Chain A: A.216, T.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.219 EOH.9: 4 residues within 4Å: Chain A: R.170, A.174 Chain B: D.113, R.116 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:R.170 Hydrogen bonds: B:D.113, B:R.116, B:R.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scott, D.E. et al., A Fragment-Based Approach to Probing Adenosine Recognition Sites by Using Dynamic Combinatorial Chemistry. Chembiochem (2009)

Release Date

2009-12-01

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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