SMTL ID : 6kqu.1

Crystal structure of phospholipase A2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: C.49, R.52, L.53, E.88, R.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.52, A:R.92, A:R.92 GOL.2: 3 residues within 4Å: Chain A: S.68 Ligands: CL.4, B3P.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.68

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

CL.3: 4 residues within 4Å: Chain A: A.45, C.49, R.52, R.92 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: S.68, V.69 Ligands: GOL.2, B3P.11 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: Y.104, N.105, R.106 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: G.73, I.74, K.91 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: D.37, Q.38, W.41 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: K.15, Q.19, R.106 Ligand excluded by PLIP

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

NA.9: 1 residues within 4Å: Chain A: T.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.81 Water bridges: A:T.81

1 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: 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.11: 7 residues within 4Å: Chain A: Q.4, K.11, Y.65, L.66, F.67 Ligands: GOL.2, CL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.4, A:Y.65, A:F.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, S. et al., Residue Asn21 acts as a switch for calcium binding to modulate the enzymatic activity of human phospholipase A2 group IIE. Biochimie (2020)

Release Date

2020-08-19

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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