SMTL ID : 4x97.2 (3 other biounits)

Crystal structure of Lysosomal Phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (MAFP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.67, T.69, S.70, Q.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.74 NAG.2: 2 residues within 4Å: Chain A: N.241, E.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.283 NAG.3: 4 residues within 4Å: Chain A: Q.252, T.255, I.256, N.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.257 NAG.4: 6 residues within 4Å: Chain A: L.355, P.356, G.357, S.358, N.366, T.368 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.366 Water bridges: A:T.369

1 x MAY: METHYL ARACHIDONYL FLUOROPHOSPHONATE(Covalent)

MAY.5: 14 residues within 4Å: Chain A: G.13, D.14, L.15, W.44, L.45, L.95, V.102, Y.105, S.166, M.167, I.216, T.330, H.360, I.361 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.15, A:L.15, A:W.44, A:L.45, A:L.95, A:Y.105, A:I.216, A:I.361, A:I.361 Hydrogen bonds: A:D.14, A:M.167

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 7 residues within 4Å: Chain A: L.32, C.33, S.34, F.41, I.54, C.57, N.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.34, A:S.34, A:N.61

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

CL.7: 3 residues within 4Å: Chain A: Q.295, H.348, Q.349 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 5 residues within 4Å: Chain A: Q.181, G.293, Q.346, E.347, H.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.181, A:Q.181, A:E.347, A:H.348 Salt bridges: A:H.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glukhova, A. et al., Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase. Nat Commun (2015)

Release Date

2015-03-11

Peptides

Group XV phospholipase A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Group XV phospholipase A2

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