SMTL ID : 4x94.1

Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (hexagonal form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.70, A:Q.74 NAG.2: 2 residues within 4Å: Chain A: N.241, E.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.283 Water bridges: A:N.241, A:R.279 NAG.3: 3 residues within 4Å: Chain A: V.249, T.255, N.257 No protein-ligand interaction detected (PLIP) NAG.4: 8 residues within 4Å: Chain A: L.355, P.356, G.357, S.358, E.362, N.366, T.368 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.362, A:E.362

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

EPE.5: 7 residues within 4Å: Chain A: L.23, C.33, S.34, F.41, L.49, C.57, N.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.34, A:N.61

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

SO4.6: 4 residues within 4Å: Chain A: V.114, Y.118, T.119, R.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120 Salt bridges: A:R.120 SO4.7: 5 residues within 4Å: Chain A: Q.181, G.293, Q.346, E.347, H.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.347, A:H.348 Salt bridges: A:H.348 SO4.8: 3 residues within 4Å: Chain A: Q.295, H.348, Q.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.295, A:Q.349, A:Q.349 Salt bridges: A:H.348 SO4.9: 4 residues within 4Å: Chain A: E.362, N.366, A.367 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.366, A:A.367 SO4.10: 4 residues within 4Å: Chain A: R.82, P.84, G.85, F.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.85 Salt bridges: A:R.82

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
A

Group XV phospholipase A2

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