SMTL ID : 2wq5.1

Non-antibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: D.39 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:D.39, H2O.3 CA.4: 1 residues within 4Å: Chain B: D.39 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.39, B:D.39, H2O.9 CA.7: 1 residues within 4Å: Chain C: D.39 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:D.39, H2O.16

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

SO4.2: 4 residues within 4Å: Chain A: Q.4, N.7, Y.69 Chain C: W.61 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:W.61, A:Q.4, A:N.7, A:Y.69 Water bridges: C:K.59, C:K.59, C:C.60 SO4.5: 4 residues within 4Å: Chain A: W.61 Chain B: Q.4, N.7, Y.69 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.4, B:N.7, B:Y.69, A:W.61 Water bridges: A:K.59, A:K.59, A:C.60 SO4.8: 4 residues within 4Å: Chain B: W.61 Chain C: Q.4, N.7, Y.69 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:W.61, C:Q.4, C:N.7, C:Y.69, C:Y.69 Water bridges: B:K.59, B:K.59, B:C.60

3 x MIY: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE(Non-covalent)

MIY.3: 13 residues within 4Å: Chain A: L.2, W.18, A.22, G.29, R.30, F.63, F.64 Chain B: L.2, Y.3, W.18 Chain C: R.30 Ligands: MIY.6, MIY.9 11 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:L.2, A:F.63, A:F.63, A:F.63, A:F.64, B:L.2, B:Y.3 Hydrogen bonds: A:A.22, A:R.30, A:R.30, C:R.30 MIY.6: 13 residues within 4Å: Chain A: R.30 Chain B: L.2, W.18, A.22, G.29, R.30, F.63, F.64 Chain C: L.2, Y.3, W.18 Ligands: MIY.3, MIY.9 11 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:L.2, B:F.63, B:F.63, B:F.63, B:F.64, C:L.2, C:Y.3 Hydrogen bonds: B:A.22, B:R.30, B:R.30, A:R.30 MIY.9: 13 residues within 4Å: Chain A: L.2, Y.3, W.18 Chain B: R.30 Chain C: L.2, W.18, A.22, G.29, R.30, F.63, F.64 Ligands: MIY.3, MIY.6 11 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:L.2, C:F.63, C:F.63, C:F.63, C:F.64, A:L.2, A:Y.3 Hydrogen bonds: C:A.22, C:R.30, C:R.30, B:R.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dalm, D. et al., Non-Antibiotic Properties of Tetracyclines: Structural Basis for Inhibition of Secretory Phospholipase A(2). J.Mol.Biol. (2010)

Release Date

2010-03-23

Peptides

PHOSPHOLIPASE A2, ACIDIC: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

PHOSPHOLIPASE A2, ACIDIC