SMTL ID : 5wzo.1

Crystal structure of human secreted phospholipase A2 group IIE, crystallized with calcium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: R.52, L.56 Ligands: GOL.12 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: S.68, V.69 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: G.73, R.98 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: A.45, C.49, R.52, R.92 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: K.15, Q.19, R.106 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.73, I.74, K.91, L.95 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Y.104, N.105, R.106 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: R.79, Q.83 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: T.80, T.81, C.82 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: Y.26, G.28, G.30, D.47 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.26, A:G.28, A:G.30, A:D.47, H2O.4 CA.11: 4 residues within 4Å: Chain A: D.22, Y.23, G.24, Y.111 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.22, A:G.24

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: C.49, R.52, L.53, E.88, C.89, R.92 Ligands: CL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.52, A:R.92, A:R.92 Water bridges: A:E.88, A:E.88 GOL.13: 6 residues within 4Å: Chain A: Q.4, K.64, Y.65, L.66, Q.83 Ligands: B3P.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.4, A:K.64, A:Q.83

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.14: 4 residues within 4Å: Chain A: Q.4, L.66, F.67 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.4, A:F.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, S. et al., Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A2 group IIE. Sci Rep (2017)

Release Date

2018-01-24

Peptides

Group IIE secretory phospholipase A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Group IIE secretory phospholipase A2

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