SMTL ID : 1fv0.3 (2 other biounits)

FIRST STRUCTURAL EVIDENCE OF THE INHIBITION OF PHOSPHOLIPASE A2 BY ARISTOLOCHIC ACID: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ARISTOLOCHIC ACID

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: Y.103, S.104, K.105 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.103, A:K.105 Water bridges: A:K.106 Salt bridges: A:K.105 SO4.2: 4 residues within 4Å: Chain A: K.37, D.38, A.39, R.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.37, A:A.39 Water bridges: A:R.42, A:R.42 Salt bridges: A:R.42 SO4.6: 3 residues within 4Å: Chain B: Y.103, S.104, K.105 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.103, B:K.105 Water bridges: B:K.106 Salt bridges: B:K.105 SO4.7: 4 residues within 4Å: Chain B: K.37, D.38, A.39, R.42 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.37, B:A.39 Water bridges: B:R.42, B:R.42 Salt bridges: B:R.42 SO4.11: 4 residues within 4Å: Chain B: R.68, G.71 Chain C: S.104, K.106 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.104 Water bridges: C:K.106, B:R.68 Salt bridges: C:K.106, B:R.68 SO4.12: 3 residues within 4Å: Chain C: K.37, D.38, R.42 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.39 Salt bridges: C:R.42 SO4.16: 4 residues within 4Å: Chain A: R.68, G.71 Chain D: S.104, K.106 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:S.104 Water bridges: D:K.106, A:R.68 Salt bridges: D:K.106, A:R.68 SO4.17: 3 residues within 4Å: Chain D: K.37, D.38, R.42 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.39 Water bridges: D:T.102 Salt bridges: D:R.42

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: N.58, P.59, K.60, S.61 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.60 Hydrogen bonds: A:K.60, A:S.61 Salt bridges: A:K.60 ACT.8: 4 residues within 4Å: Chain B: N.58, P.59, K.60, S.61 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.60 Hydrogen bonds: B:K.60, B:S.61 Salt bridges: B:K.60

2 x 9AR: 9-HYDROXY ARISTOLOCHIC ACID(Non-covalent)

9AR.4: 15 residues within 4Å: Chain A: L.2, F.5, I.9, A.17, I.18, Y.21, S.22, Y.27, G.29, W.30, C.44, H.47, D.48, Y.51, K.60 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.2, A:F.5, A:I.18 Hydrogen bonds: A:C.44 Water bridges: A:G.29, A:G.29 9AR.9: 15 residues within 4Å: Chain B: L.2, F.5, I.9, A.17, I.18, Y.21, S.22, Y.27, G.29, W.30, C.44, H.47, D.48, Y.51, K.60 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.2, B:F.5, B:I.18 Hydrogen bonds: B:C.44, B:H.47 Water bridges: B:G.29, B:G.29

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Y.110, P.111, L.114 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.109 GOL.10: 3 residues within 4Å: Chain B: Y.110, P.111, L.114 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.109 GOL.15: 1 residues within 4Å: Chain C: E.11 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.7 GOL.20: 1 residues within 4Å: Chain D: E.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.11 Water bridges: D:K.7

4 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.13: 4 residues within 4Å: Chain C: R.97, L.100, N.101 Ligands: DIO.14 No protein-ligand interaction detected (PLIP) DIO.14: 3 residues within 4Å: Chain C: Q.98, N.101 Ligands: DIO.13 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.101 DIO.18: 4 residues within 4Å: Chain D: R.97, L.100, N.101 Ligands: DIO.19 No protein-ligand interaction detected (PLIP) DIO.19: 3 residues within 4Å: Chain D: Q.98, N.101 Ligands: DIO.18 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandra, V. et al., Structural Basis of Phospholipase A2 Inhibition for the Synthesis of Prostaglandins by the Plant Alkaloid Aristolochic Acid from a 1.7 A Crystal Structure. Biochemistry (2002)

Release Date

2002-08-28

Peptides

PHOSPHOLIPASE A2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

PHOSPHOLIPASE A2

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