SMTL ID : 7jrw.1

Phospholipase D engineered mutant bound to phosphatidic acid (5 day soak)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 9 residues within 4Å: Chain A: A.122, S.156, M.157, T.158, P.231, A.232, K.233, V.234, W.235 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.235, A:W.235

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: Q.49, T.50, P.51, G.52, C.53, W.54, S.199, D.200, H.443 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.49, A:T.50, A:G.52, A:C.53, A:C.53, A:D.200, A:H.443 Water bridges: A:S.427

1 x VHY: (2R)-3-(phosphonooxy)propane-1,2-diyl dibutanoate(Non-covalent)

VHY.3: 14 residues within 4Å: Chain A: L.88, A.123, L.164, W.166, H.168, Q.337, L.346, V.380, G.381, H.442, K.444, N.459, Y.461, L.465 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.123, A:L.164, A:W.166, A:W.166, A:L.346 Hydrogen bonds: A:Q.337, A:N.459, A:Y.461 Water bridges: A:H.168, A:K.170, A:Q.337, A:G.381 Salt bridges: A:H.168, A:H.168, A:H.442, A:K.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samantha, A. et al., Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation. Biochem.J. (2021)

Release Date

2021-04-28

Peptides

Phospholipase D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phospholipase D

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