SMTL ID : 6zth.1

Phospholipase PlaB from Legionella pneumophila

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 19 residues within 4Å: Chain A: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Chain C: Y.358, D.359, L.360, R.381, R.383, L.391, Y.393 Ligands: NAD.2, NAD.5 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:R.145, A:N.209, A:S.210, A:Y.211, A:Q.382, C:L.360, C:L.360, C:R.381, C:R.383 Water bridges: A:D.380 pi-Stacking: A:Y.211 Salt bridges: C:R.381 NAD.2: 24 residues within 4Å: Chain A: I.200, R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Chain C: L.360, Y.361, L.362, E.370, Q.371, A.372, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Ligands: NAD.1 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:Y.205, A:Y.335 Hydrogen bonds: A:R.202, A:R.202, A:Y.205, A:Y.205, A:A.207, A:S.210, C:L.362, C:L.362, C:E.370, C:G.376, C:R.381 pi-Stacking: A:Y.205, C:F.377 NAD.3: 26 residues within 4Å: Chain B: I.200, R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Chain D: L.360, Y.361, L.362, T.363, E.370, Q.371, A.372, L.373, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Ligands: NAD.7 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:Y.335 Hydrogen bonds: B:R.202, B:R.202, B:Y.205, B:A.207, B:S.210, B:S.210, B:S.210, D:L.362, D:E.370, D:E.370, D:L.373, D:G.376, D:R.381, D:Y.393 pi-Stacking: B:Y.205, D:F.377 NAD.4: 25 residues within 4Å: Chain B: L.360, Y.361, L.362, E.370, Q.371, A.372, L.373, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Chain D: I.200, R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Ligands: NAD.8 18 PLIP interactions: 10 interactions with chain D, 8 interactions with chain B Hydrophobic interactions: D:Y.335 Hydrogen bonds: D:R.202, D:R.202, D:Y.205, D:Y.205, D:A.207, D:S.210, D:S.210, D:S.210, B:L.362, B:E.370, B:E.370, B:L.373, B:G.376, B:R.381, B:Y.393 pi-Stacking: D:Y.205, B:F.377 NAD.5: 19 residues within 4Å: Chain A: Y.358, D.359, L.360, R.381, R.383, L.391, Y.393 Chain C: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Ligands: NAD.1, NAD.6 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:R.145, C:N.209, C:S.210, C:Y.211, C:Q.382, A:L.360, A:R.381, A:R.381, A:R.381, A:R.383, A:Y.393 Water bridges: C:R.145, C:R.145 Salt bridges: C:R.145 pi-Stacking: C:Y.211 NAD.6: 24 residues within 4Å: Chain A: L.360, Y.361, L.362, E.370, Q.371, A.372, L.373, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Chain C: R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Ligands: NAD.5 16 PLIP interactions: 6 interactions with chain C, 10 interactions with chain A Hydrogen bonds: C:R.202, C:R.202, C:Y.205, C:Y.205, C:A.207, A:L.362, A:L.362, A:E.370, A:L.373, A:G.376, A:R.381, A:R.381, A:Y.393 pi-Stacking: C:Y.205, A:F.377 Water bridges: A:R.381 NAD.7: 19 residues within 4Å: Chain B: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Chain D: Y.358, D.359, L.360, R.381, R.383, L.391, Y.393 Ligands: NAD.3, NAD.8 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain D Hydrogen bonds: B:R.145, B:R.145, B:N.209, B:S.210, B:Y.211, B:Q.382, D:L.360, D:R.381, D:R.383, D:R.383, D:Y.393 pi-Stacking: B:Y.211 Salt bridges: D:R.381, D:R.381 NAD.8: 19 residues within 4Å: Chain B: Y.358, D.359, L.360, R.381, R.383, L.391, Y.393 Chain D: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Ligands: NAD.4, NAD.7 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:R.145, D:R.145, D:N.209, D:S.210, D:S.210, D:Y.211, B:L.360, B:R.383 Salt bridges: D:R.145, B:R.381 pi-Stacking: D:Y.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diwo, M. et al., NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-06-02

Peptides

PlaB phospholipase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PlaB phospholipase

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