SMTL ID : 4x91.4 (3 other biounits)

Crystal structure of Lysosomal Phospholipase A2 in complex with Isopropyl dodec-11-enylfluorophosphonate (IDFP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.67, S.70, Q.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67, 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:N.241, A:E.283 Water bridges: A:N.241 NAG.3: 5 residues within 4Å: Chain A: V.249, Q.252, T.255, I.256, N.257 No protein-ligand interaction detected (PLIP) NAG.4: 7 residues within 4Å: Chain A: L.355, P.356, G.357, S.358, E.362, N.366, T.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.366 Water bridges: A:S.358, A:S.358, A:E.359

1 x TO4: propan-2-yl (R)-dodec-11-en-1-ylphosphonofluoridate(Covalent)

TO4.5: 15 residues within 4Å: Chain A: G.13, D.14, L.15, L.95, V.102, Y.105, S.166, M.167, P.197, V.201, I.216, T.330, H.360, I.361 Ligands: MPD.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.15, A:L.95, A:V.102, A:Y.105, A:P.197, A:V.201, A:V.201, A:I.216, A:T.330, 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: C.33, S.34, F.41, L.49, I.54, C.57, N.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.34, A:N.61

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

PO4.7: 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:G.293, A:E.347, A:H.348 Salt bridges: A:H.348 PO4.8: 3 residues within 4Å: Chain A: Q.295, H.348, Q.349 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.295, A:E.347, A:Q.349, A:Q.349 Salt bridges: A:H.348

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 9 residues within 4Å: Chain A: L.15, W.44, D.212, N.214, I.216, I.224, Q.227, Q.228 Ligands: TO4.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.15, A:N.214, A:I.216 Hydrogen bonds: A:Q.227, A:Q.228

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
D

Group XV phospholipase A2

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