SMTL ID : 5y5e.1

Crystal structure of phospholipase A2 with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: C.49, R.52, L.53, E.88, C.89, R.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.52, A:R.52, A:R.92, A:R.92

1 x 7W3: 2-[2-methyl-3-oxamoyl-1-[[2-(trifluoromethyl)phenyl]methyl]indol-4-yl]oxyethanoic acid(Non-covalent)

7W3.2: 18 residues within 4Å: Chain A: F.5, G.6, I.9, A.17, L.18, Y.20, G.21, Y.26, C.27, G.28, I.29, G.30, C.43, H.46, D.47, K.61, F.97 Ligands: CA.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.5, A:I.9, A:F.97 Hydrogen bonds: A:G.28, A:G.30, A:D.47 Water bridges: A:D.47, A:D.47 Salt bridges: A:K.61 Halogen bonds: A:A.17

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

CL.3: 3 residues within 4Å: Chain A: D.37, Q.38, W.41 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: Y.104, N.105, R.106 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: S.68, V.69 Ligands: B3P.9 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.45, C.49, R.52, R.92 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: G.73, I.74, K.91, L.95 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: Y.26, G.28, G.30, D.47 Ligands: 7W3.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.26, A:G.28, A:G.30, A:D.47, A:D.47

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

B3P.9: 5 residues within 4Å: Chain A: Q.4, Y.65, L.66, F.67 Ligands: CL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.4, A:Y.65, A:F.67

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 1 residues within 4Å: Chain A: T.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.81, A:T.81 Water bridges: A:T.81

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 A2group IIE. Sci Rep (2017)

Release Date

2018-06-20

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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