SMTL ID : 4x91.1 (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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.283 Water bridges: A:R.279 NAG.3: 6 residues within 4Å: Chain A: V.249, Q.252, P.254, T.255, I.256, N.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.252 NAG.4: 6 residues within 4Å: Chain A: L.355, P.356, G.357, S.358, N.366, T.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.366 Water bridges: A:E.359, A:E.359, A:T.369

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

TO4.5: 16 residues within 4Å: Chain A: G.13, D.14, L.15, H.165, S.166, M.167, P.197, V.201, T.204, V.207, Q.227, A.231, T.234, L.237, T.330, H.360 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.15, A:V.201, A:T.204, A:V.207, A:A.231, A:L.237, A:T.330 Hydrogen bonds: A:D.14, A:M.167

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

EPE.6: 6 residues within 4Å: Chain A: C.33, S.34, F.41, I.54, C.57, N.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.34, A:N.61

4 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.181, A:Q.181, A:G.293, A:E.347, A:H.348 Salt bridges: A:H.348 PO4.8: 4 residues within 4Å: Chain A: Q.295, E.347, 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 PO4.9: 3 residues within 4Å: Chain A: R.264, W.276, Q.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.276, A:W.276, A:Q.280 Salt bridges: A:R.264 PO4.10: 5 residues within 4Å: Chain A: K.88, T.89, F.90, R.120, G.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.89, A:T.89, A:F.90, A:R.120

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

MPD.11: 7 residues within 4Å: Chain A: L.15, W.44, W.58, R.215, I.224, Q.227, Q.228 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.15, A:L.15, A:W.44, A:W.58, A:R.215, A:I.224 Hydrogen bonds: A:Q.227, A:Q.228 MPD.12: 1 residues within 4Å: Chain A: Q.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.74

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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