SMTL ID : 7l27.1 (1 other biounit)

Crystal structure of the catalytic domain of human PDE3A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.89, H.154, D.155, D.268 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.89, A:H.154, A:D.155, A:D.268, H2O.1, H2O.4 MN.4: 5 residues within 4Å: Chain B: H.89, H.154, D.155, D.268 Ligands: MG.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.89, B:D.155, B:D.268, H2O.6, H2O.9

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.155 Ligands: MN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.155, H2O.1, H2O.3, H2O.3, H2O.4, H2O.5 MG.5: 2 residues within 4Å: Chain B: D.155 Ligands: MN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.155, H2O.6, H2O.8, H2O.8, H2O.9, H2O.9

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

ACT.3: 9 residues within 4Å: Chain A: V.33, I.36, G.37, K.39, C.40, 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:K.39, A:G.41, A:R.42, A:I.43 Salt bridges: A:R.87 ACT.6: 8 residues within 4Å: Chain B: V.33, G.37, K.39, C.40, 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

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