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

Structure of human Phospholipase D2 catalytic domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: K.110, K.124, R.138, K.277, K.279, Y.280 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.280 Water bridges: A:K.124 Salt bridges: A:K.110, A:K.124, A:R.138, A:K.277, A:K.279 SO4.2: 3 residues within 4Å: Chain A: W.380, C.381, N.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.381, A:N.509 Water bridges: A:H.342 SO4.3: 3 residues within 4Å: Chain A: H.28, R.29, P.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29 Salt bridges: A:H.28 SO4.4: 4 residues within 4Å: Chain A: K.429, T.434, W.436, R.437 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.436 Salt bridges: A:K.429, A:R.437 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 SO4.6: 5 residues within 4Å: Chain A: V.46, N.47, A.49, D.174, L.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.47, A:L.175 Water bridges: A:A.49 SO4.7: 4 residues within 4Å: Chain A: E.113, G.121, R.125, R.138 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.121, A:R.125 Water bridges: A:N.119, A:S.120 Salt bridges: A:R.138 SO4.8: 5 residues within 4Å: Chain A: K.524, L.539, D.540, L.541, R.542 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.539, A:L.541 Salt bridges: A:K.524

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: W.71, H.149, K.151, D.166, R.171, Q.349, H.463, K.465, N.480 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.151, A:D.166, A:D.166, A:R.171, A:K.465, A:K.465, A:N.480 GOL.10: 6 residues within 4Å: Chain A: R.437, N.574, H.612, F.613, L.615, K.616 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.437, A:N.574, A:N.574, A:L.615 GOL.11: 7 residues within 4Å: Chain A: H.411, R.419, L.618, E.619, E.621, S.622, L.623 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.411, A:R.419, A:L.618, A:E.621 GOL.12: 3 residues within 4Å: Chain A: Q.341, R.371, W.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.341, A:Q.341, A:R.371, A:R.371

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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