SMTL ID : 6h5a.1

Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) in complex with manganese and citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

7 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 5 residues within 4Å: Chain A: T.34, D.68, D.71, D.89 Ligands: MN.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.68, A:D.68, A:D.71, A:D.89, H2O.2, H2O.2 MN.2: 6 residues within 4Å: Chain A: D.68, D.89, D.93, R.152 Ligands: MN.1, FLC.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.68, A:D.68, A:D.89, A:D.93, A:D.93 MN.3: 3 residues within 4Å: Ligands: MN.4, FLC.5, FLC.6 No protein-ligand interaction detected (PLIP) MN.4: 4 residues within 4Å: Chain A: R.152 Ligands: MN.3, FLC.5, FLC.6 No protein-ligand interaction detected (PLIP) MN.11: 4 residues within 4Å: Chain B: K.135, E.151, R.195 Ligands: FLC.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.151, H2O.5 MN.12: 4 residues within 4Å: Chain B: D.68, D.71, D.89 Ligands: MN.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.68, B:D.68, B:D.71, B:D.89, H2O.3 MN.13: 4 residues within 4Å: Chain B: D.68, D.89, D.93 Ligands: MN.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.68, B:D.89, B:D.93, B:D.93, H2O.3

3 x FLC: CITRATE ANION(Non-covalent)

FLC.5: 12 residues within 4Å: Chain A: R.9, D.68, D.89, D.93, E.151, R.152, P.153 Chain B: F.222 Ligands: MN.2, MN.3, MN.4, FLC.6 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Water bridges: A:R.9, A:R.94, A:K.135, A:R.152, A:R.152 Salt bridges: A:R.152 Hydrophobic interactions: B:F.222 FLC.6: 13 residues within 4Å: Chain A: A.90, R.94, I.131, S.132, K.135, R.152, R.155, R.195 Chain B: Y.133, R.137 Ligands: MN.3, MN.4, FLC.5 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.90 Hydrogen bonds: A:S.132, A:S.132 Water bridges: A:A.90, A:K.135, A:R.152, A:R.155, A:R.195, A:R.195, B:R.137 Salt bridges: A:R.94, A:K.135, A:R.195, B:R.137 FLC.14: 10 residues within 4Å: Chain A: Y.133 Chain B: R.94, I.131, S.132, K.135, E.151, R.152, R.155, R.195 Ligands: MN.11 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.132, B:S.132, B:R.152 Water bridges: B:S.132, B:K.135, B:A.136 Salt bridges: B:R.94, B:K.135, B:K.135, B:R.155, B:R.195, B:R.195

3 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.7: 16 residues within 4Å: Chain A: L.46, P.50, I.95, A.99, C.102, W.106 Chain B: R.115, P.116, I.119, L.122, I.123, V.126, T.127, V.189, C.192 Ligands: LFA.10 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.95, A:I.95, B:L.122, B:L.122, B:I.123, B:V.189 OLC.8: 16 residues within 4Å: Chain A: P.5, L.7, S.8, R.9, A.10, F.55, A.58, C.59, W.62, E.154, I.157, L.160, T.161, G.164, V.165, F.168 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.58, A:W.62, A:W.62, A:W.62, A:I.157, A:L.160 Hydrogen bonds: A:R.9 Water bridges: A:S.8, A:A.10 OLC.15: 9 residues within 4Å: Chain B: D.114, P.116, L.117, P.175, S.178, V.179, W.182, L.183, V.186 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.179, B:W.182, B:W.182, B:W.182 Hydrogen bonds: B:S.178, B:S.178, B:W.182 Water bridges: B:D.114

4 x LFA: EICOSANE(Non-covalent)

LFA.9: 9 residues within 4Å: Chain A: A.40, A.43, G.44, T.47, L.48, M.51, K.53, V.60, F.64 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.47, A:L.48 LFA.10: 15 residues within 4Å: Chain A: I.35, T.38, T.39, V.42, A.43, L.46, F.84, L.88, C.92, I.95 Chain B: V.193, L.196, H.197, W.200 Ligands: OLC.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.196, B:W.200, A:V.42 LFA.17: 19 residues within 4Å: Chain A: I.119, L.122, I.123, V.126, T.127, V.130, V.189, C.192, V.193, L.196 Chain B: V.42, L.46, P.50, I.95, G.98, A.99, C.102, G.103, W.106 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.122, A:L.122, A:I.123, A:V.126, B:L.46, B:I.95, B:I.95, B:W.106, B:W.106, B:W.106 LFA.20: 8 residues within 4Å: Chain B: A.40, A.43, G.44, T.47, L.48, M.51, V.60, F.64 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.48

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

SO4.16: 3 residues within 4Å: Chain A: R.14 Chain B: R.217, N.219 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.219, B:N.219 Water bridges: B:R.217 Salt bridges: B:R.217, A:R.14

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.18: 9 residues within 4Å: Chain B: G.52, L.54, W.107, H.111, M.112, S.166, D.167, P.174, L.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.107 1PE.19: 5 residues within 4Å: Chain A: R.208, M.209, A.210 Chain B: G.79, G.80 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grave, K. et al., Structure ofMycobacterium tuberculosisphosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis. Commun Biol (2019)

Release Date

2019-05-15

Peptides

CDP-diacylglycerol--inositol 3-phosphatidyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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CDP-diacylglycerol--inositol 3-phosphatidyltransferase