SMTL ID : 7l28.1 (1 other biounit)

Crystal structure of the catalytic domain of human PDE3A bound to Trequinsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x XKG: (2E)-9,10-dimethoxy-3-methyl-2-[(2,4,6-trimethylphenyl)imino]-2,3,6,7-tetrahydro-4H-pyrimido[6,1-a]isoquinolin-4-one(Non-covalent)

XKG.1: 10 residues within 4Å: Chain A: Y.84, T.162, P.272, I.286, F.290, L.318, Q.319, S.321, F.322, I.326 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.322, A:F.322, A:I.326 pi-Stacking: A:F.290, A:F.322 XKG.5: 9 residues within 4Å: Chain B: Y.84, T.162, P.272, I.286, F.290, L.318, Q.319, S.321, F.322 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.286, B:F.290, B:F.322, B:F.322 Water bridges: B:Q.319 pi-Stacking: B:F.290, B:F.322

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: H.89, H.154, D.155, D.268 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.89, A:H.154, A:D.155, A:D.268, H2O.1 MN.6: 5 residues within 4Å: Chain B: H.89, H.154, D.155, D.268 Ligands: MG.7 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.89, B:H.154, B:D.155, B:D.268, H2O.2, H2O.2

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.155 Ligands: MN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.155, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.7: 2 residues within 4Å: Chain B: D.155 Ligands: MN.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.155, H2O.2, H2O.2, H2O.2, H2O.2

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

ACT.4: 8 residues within 4Å: Chain A: V.33, G.37, R.38, K.39, G.41, R.42, I.43, R.87 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.33, A:I.43 Hydrogen bonds: A:C.40, A:G.41, A:R.42, A:I.43 Salt bridges: A:R.87 ACT.8: 8 residues within 4Å: Chain B: V.33, G.37, R.38, K.39, G.41, R.42, I.43, R.87 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.33 Hydrogen bonds: B:K.39, B:G.41, B:R.42, B:I.43 Salt bridges: B:R.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garvie, C.W. et al., Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun (2021)

Release Date

2021-06-16

Peptides

cGMP-inhibited 3',5'-cyclic phosphodiesterase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

cGMP-inhibited 3',5'-cyclic phosphodiesterase A

Related Entries With Identical Sequence