SMTL ID : 3u8h.3 (2 other biounits)

Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x BHP: (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PHENYL-HEPTANOYLAMINO)-PENTANOIC ACID(Non-covalent)

BHP.1: 22 residues within 4Å: Chain A: L.2, F.5, H.6, I.9, A.17, A.18, Y.21, G.22, H.27, C.28, G.29, V.30, G.31, C.44, H.47, D.48, Y.51, K.62 Chain B: F.23, V.30 Ligands: CA.3, BHP.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.2, A:F.5, A:H.6, A:I.9, A:A.17, A:Y.21, A:V.30, A:Y.51, A:Y.51 Hydrogen bonds: A:G.29, A:G.31, A:H.47 BHP.6: 22 residues within 4Å: Chain A: A.18, F.23 Chain B: L.2, F.5, H.6, I.9, A.17, A.18, Y.21, G.22, F.23, H.27, C.28, G.29, V.30, G.31, C.44, H.47, D.48, Y.51 Ligands: BHP.1, CA.8 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.2, B:F.5, B:F.5, B:H.6, B:I.9, B:A.17, B:A.18, B:Y.21, B:F.23, B:Y.51, B:Y.51, A:A.18, A:F.23 Hydrogen bonds: B:G.29, B:G.31, B:D.48

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: F.23, Y.24, G.25, Y.112, N.114 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.23, A:G.25, A:Y.112, H2O.7, H2O.23 CA.3: 5 residues within 4Å: Chain A: H.27, G.29, G.31, D.48 Ligands: BHP.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.27, A:G.29, A:G.31, A:D.48, A:D.48 CA.7: 4 residues within 4Å: Chain B: F.23, G.25, Y.112, N.114 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.23, B:G.25, B:Y.112, H2O.62, H2O.87 CA.8: 5 residues within 4Å: Chain B: H.27, G.29, G.31, D.48 Ligands: BHP.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.27, B:G.29, B:G.31, B:D.48, B:D.48

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

CL.4: 3 residues within 4Å: Chain A: N.4, R.7, F.68 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: F.63, L.64, S.65, R.84 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: N.4, R.7, F.68 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: F.63, L.64, S.65, R.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, L.K. et al., Selective Inhibition of Human Group IIA-secreted Phospholipase A2 (hGIIA) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of hGIIA to Vimentin in Rheumatoid Synoviocytes. J.Biol.Chem. (2013)

Release Date

2012-10-17

Peptides

Phospholipase A2, membrane associated: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phospholipase A2, membrane associated

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