SMTL ID : 6ohm.1 (1 other biounit)

Structure of tungstate bound human Phospholipase D2 catalytic domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x WO4: TUNGSTATE(VI)ION(Non-covalent)

WO4.1: 7 residues within 4Å: Chain A: H.149, K.151, D.166, Q.349, H.463, K.465, N.480 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Water interactions Hydrogen bonds: A:K.151, A:D.166, A:Q.349, A:K.465, A:K.465, A:N.480 Water bridges: A:R.171 Metal complexes: A:H.149, H2O.1

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

SO4.2: 5 residues within 4Å: Chain A: K.124, R.138, K.277, K.279, Y.280 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.136, A:Y.280 Salt bridges: A:K.124, A:R.138, A:K.277, A:K.279 SO4.3: 4 residues within 4Å: Chain A: E.113, G.121, R.125, R.138 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.110, A:G.121, A:G.121, A:R.125, A:R.138 Salt bridges: A:R.125, A:R.138 SO4.4: 5 residues within 4Å: Chain A: K.524, L.539, D.540, L.541, R.542 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.539, A:L.541, A:R.542 Water bridges: A:K.524, A:K.524 Salt bridges: A:K.524 SO4.5: 5 residues within 4Å: Chain A: H.139, P.140, D.141, Q.142, T.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.141, A:Q.142 Salt bridges: A:H.139

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain A: W.380, C.381, N.509, I.545 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.381, A:N.509 Water bridges: A:H.342 GOL.8: 3 residues within 4Å: Chain A: H.28, R.29, P.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.28, A:R.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metrick, C.M. et al., Human PLD structures enable drug design and characterization of isoenzyme selectivity. Nat.Chem.Biol. (2020)

Release Date

2020-02-19

Peptides

Phospholipase D2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phospholipase D2

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