SMTL ID : 6h59.1

Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) with CDP-DAG bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.68, D.89, C.92, D.93 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.89, A:D.89, A:D.93, H2O.1, H2O.1 MG.2: 5 residues within 4Å: Chain A: D.68, D.71, G.72, D.89 Ligands: FQT.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.68, A:D.68, A:D.71, A:D.89 MG.20: 5 residues within 4Å: Chain B: D.68, M.69, D.71, G.72 Ligands: FQT.25 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.68, B:D.68, B:D.71, H2O.3 MG.21: 4 residues within 4Å: Chain B: D.89, A.90, D.93 Ligands: FQT.25 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.89, B:D.93, H2O.3, H2O.3, H2O.4

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

SO4.3: 4 residues within 4Å: Chain A: Y.133, R.137 Chain B: A.90, K.135 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Water bridges: B:D.89, B:D.89, B:A.90, B:D.93, B:R.94, B:R.94, B:K.135, B:K.135 Salt bridges: B:K.135, A:R.137 SO4.4: 8 residues within 4Å: Chain A: R.94, I.131, S.132, K.135, E.151, R.152, R.155, R.195 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.132, A:R.152 Water bridges: A:R.94, A:R.94 Salt bridges: A:R.94, A:R.155, A:R.195 SO4.5: 3 residues within 4Å: Chain A: P.18, R.21, R.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.18 Salt bridges: A:R.21, A:R.25 SO4.6: 4 residues within 4Å: Chain A: R.113, R.115 Chain B: F.110, R.113 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:R.113, B:R.113 Salt bridges: A:R.113, A:R.115, B:R.113 SO4.7: 2 residues within 4Å: Chain A: R.208 Chain B: R.78 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.208, B:R.78 SO4.18: 4 residues within 4Å: Chain A: W.106, H.111 Chain B: R.115 Ligands: OLB.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.106 Salt bridges: A:H.111, B:R.115 SO4.19: 4 residues within 4Å: Chain A: R.115 Chain B: W.106, H.111 Ligands: OLB.32 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.115, B:H.111 Hydrogen bonds: B:W.106 SO4.22: 8 residues within 4Å: Chain B: R.94, I.131, S.132, K.135, E.151, R.152, R.155, R.195 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.132, B:R.152 Water bridges: B:R.94, B:R.94, B:R.94 Salt bridges: B:R.94, B:R.155, B:R.195 SO4.23: 4 residues within 4Å: Chain A: A.90, K.135 Chain B: Y.133, R.137 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.133 Water bridges: B:Y.133, B:Y.133, A:A.90, A:R.94, A:K.135 Salt bridges: B:R.137, A:K.135 SO4.24: 4 residues within 4Å: Chain A: F.110, R.113 Chain B: R.113, R.115 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Water bridges: B:R.113, B:R.113, B:R.115, B:R.115 Salt bridges: B:R.113, B:R.115, A:R.113

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 8 residues within 4Å: Chain A: G.52, L.54, W.107, M.112, S.166, D.167, P.174, L.177 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.177

2 x FQT: [(2~{S})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-1,4-dihydropyrimidin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-hexanoyloxy-propyl] hexanoate(Non-covalent)

FQT.9: 23 residues within 4Å: Chain A: P.30, D.31, T.34, W.62, V.65, L.66, D.68, M.69, D.71, G.72, A.75, R.76, G.81, T.82, G.85, A.86, L.88, D.89, R.152, P.153, L.156, I.157 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.62, A:V.65, A:D.71, A:L.156 Hydrogen bonds: A:D.31, A:T.34, A:D.68, A:G.72, A:R.76, A:T.82, A:R.152 Water bridges: A:A.86 Salt bridges: A:R.76 FQT.25: 24 residues within 4Å: Chain A: M.209, I.211 Chain B: P.30, D.31, T.34, W.62, V.65, L.66, D.68, M.69, D.71, G.72, A.75, G.81, T.82, G.85, A.86, L.88, D.89, R.152, P.153, L.156 Ligands: MG.20, MG.21 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.66, B:D.71 Hydrogen bonds: B:D.31, B:D.31, B:D.31, B:G.72, B:T.82, B:R.152 Water bridges: B:M.69, B:A.73

14 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.10: 14 residues within 4Å: Chain A: V.42, L.46, P.50, I.95, G.98, A.99, C.102, G.103, W.106 Chain B: I.119, L.122, I.123, V.126 Ligands: SO4.18 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.106 Hydrophobic interactions: B:L.122, B:I.123 OLB.11: 5 residues within 4Å: Chain A: V.165, V.171, P.172, W.173 Ligands: OLB.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.173 OLB.12: 6 residues within 4Å: Chain A: P.116, I.119, I.123, W.182 Ligands: OLB.13, OLB.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.116, A:I.119, A:W.182 OLB.13: 6 residues within 4Å: Chain A: I.123, A.185, V.186, V.189, I.190 Ligands: OLB.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.186 OLB.14: 3 residues within 4Å: Chain A: P.116, W.182 Ligands: OLB.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.182 OLB.15: 3 residues within 4Å: Chain A: W.173 Ligands: OLB.11, OLB.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.173, A:W.173 OLB.16: 11 residues within 4Å: Chain A: I.157, I.158, T.161, G.162, V.165, W.173, A.176, V.179, G.180, L.183 Ligands: OLB.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.161, A:A.176, A:V.179 OLB.17: 6 residues within 4Å: Chain A: I.35, T.38, T.39, V.42, C.92, I.95 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.42 OLB.26: 11 residues within 4Å: Chain B: I.157, I.158, T.161, G.162, V.165, W.173, A.176, V.179, G.180, L.183 Ligands: OLB.27 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.157, B:T.161, B:A.176 OLB.27: 6 residues within 4Å: Chain B: V.165, F.168, V.171, P.172, W.173 Ligands: OLB.26 1 PLIP interactions: 1 interactions with chain B Water bridges: B:P.172 OLB.28: 5 residues within 4Å: Chain B: V.42, A.43, L.46, T.47 Ligands: OLB.32 No protein-ligand interaction detected (PLIP) OLB.29: 7 residues within 4Å: Chain B: I.123, W.182, A.185, V.186, V.189, I.190 Ligands: OLB.30 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.123, B:W.182, B:V.186, B:V.189 OLB.30: 3 residues within 4Å: Chain B: P.116, W.182 Ligands: OLB.29 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.116, B:W.182, B:W.182, B:W.182 OLB.32: 15 residues within 4Å: Chain A: I.119, L.122, I.123, V.126 Chain B: V.42, L.46, P.50, I.95, G.98, A.99, C.102, G.103, W.106 Ligands: SO4.19, OLB.28 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.123

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

1PE.31: 9 residues within 4Å: Chain B: G.52, L.54, W.107, M.112, S.166, D.167, P.174, P.175, L.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.107

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

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