SMTL ID : 4qvh.1

Crystal structure of the essential Mycobacterium tuberculosis phosphopantetheinyl transferase PptT, solved as a fusion protein with maltose binding protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 16 residues within 4Å: Chain A: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341, R.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:Y.156, A:R.345 GLC-GLC.9: 16 residues within 4Å: Chain B: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341, R.345 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.63, B:R.67, B:R.67, B:Y.156, B:R.345

2 x COA: COENZYME A(Non-covalent)

COA.2: 24 residues within 4Å: Chain A: R.419, R.427, K.446, D.448, K.449, G.450, E.451, P.452, L.462, T.463, H.464, D.485, E.487, K.527, E.528, Y.531, K.532, F.535, W.541, L.542, G.543, F.544, A.547 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.531, A:Y.531, A:W.541 Hydrogen bonds: A:K.449, A:T.463, A:H.464, A:Y.531, A:K.532, A:L.542 Water bridges: A:R.419, A:R.419, A:H.464, A:E.528, A:E.528 Salt bridges: A:R.419, A:R.427, A:K.446, A:H.464, A:H.464, A:K.532, A:K.532 COA.10: 24 residues within 4Å: Chain B: R.419, R.427, K.446, D.448, K.449, G.450, E.451, P.452, L.462, T.463, H.464, D.485, E.487, K.527, E.528, Y.531, K.532, F.535, W.541, L.542, G.543, F.544, A.547 Ligands: MG.11 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.531, B:Y.531, B:W.541 Hydrogen bonds: B:K.449, B:T.463, B:T.463, B:H.464, B:Y.531, B:K.532, B:L.542, A:K.449 Water bridges: B:H.464, B:H.464, B:E.528, B:E.528 Salt bridges: B:R.419, B:R.427, B:K.446, B:H.464, B:H.464, B:K.532, B:K.532

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: T.463, D.485, A.486, E.487, E.528 Ligands: COA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.485, A:A.486, A:E.487, H2O.3 MG.11: 5 residues within 4Å: Chain B: D.485, A.486, E.487, E.528 Ligands: COA.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.485, B:A.486, B:E.487, H2O.17

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 11 residues within 4Å: Chain A: P.410, L.411, I.412, A.413, R.414, S.415 Chain B: G.447, D.448, E.451, C.453, K.539 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.413, A:R.414, A:R.414, B:D.448, B:D.448, B:K.539 Water bridges: B:W.454 GOL.5: 6 residues within 4Å: Chain A: M.372, T.373, V.374, G.375, E.394, Y.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.374, A:G.375, A:E.394 Water bridges: A:E.394 GOL.6: 11 residues within 4Å: Chain A: G.447, D.448, E.451, C.453, K.539 Chain B: P.410, L.411, I.412, A.413, R.414, S.415 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.448, A:D.448, A:K.539, B:A.413, B:R.414, B:R.414 Water bridges: A:D.448, A:W.454 GOL.7: 4 residues within 4Å: Chain A: N.295, K.296, P.299, R.317 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.295, A:K.296, A:R.317 Water bridges: A:D.237, A:D.237, A:R.317, A:R.317 GOL.12: 7 residues within 4Å: Chain B: M.372, T.373, V.374, G.375, E.394, L.395, Y.396 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.374, B:G.375, B:E.394 Water bridges: B:E.394, B:Y.396 GOL.13: 3 residues within 4Å: Chain B: H.548, R.565, L.567 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.548, B:R.565, B:R.565 GOL.14: 6 residues within 4Å: Chain B: R.480, P.576, P.577, L.578, T.579, T.580 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.480, B:P.576, B:T.579, B:T.580, B:T.580 Water bridges: B:T.580

2 x FLC: CITRATE ANION(Non-covalent)

FLC.8: 7 residues within 4Å: Chain A: V.416, R.419, E.422 Chain B: D.448, K.449, F.535, K.539 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Water bridges: A:R.419, A:R.419, A:E.422, A:K.446, B:K.449, B:K.449 Salt bridges: A:R.419, A:K.446, B:K.449, B:K.449 Hydrophobic interactions: B:D.448 Hydrogen bonds: B:K.449 FLC.15: 6 residues within 4Å: Chain A: D.448, K.449, F.535, K.539 Chain B: V.416, R.419 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.448 Hydrogen bonds: A:K.449 Water bridges: A:K.449, A:K.449 Salt bridges: A:K.449, A:K.449, B:R.419, B:K.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, J. et al., Crystal structure of the essential Mycobacterium tuberculosis phosphopantetheinyl transferase PptT, solved as a fusion protein with maltose binding protein. J.Struct.Biol. (2014)

Release Date

2014-12-17

Peptides

Maltose-binding periplasmic protein, 4'-phosphopantetheinyl transferase chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Maltose-binding periplasmic protein, 4'-phosphopantetheinyl transferase chimera