SMTL ID : 7kwe.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x X5M: (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one(Non-covalent)

X5M.1: 13 residues within 4Å: Chain A: Y.84, L.228, I.269, G.271, P.272, H.279, W.282, T.283, I.286, F.290, L.318, Q.319, F.322 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.84, A:W.282, A:I.286, A:F.322 Hydrogen bonds: A:H.279, A:Q.319, A:Q.319 pi-Stacking: A:F.322 X5M.5: 13 residues within 4Å: Chain B: Y.84, L.228, I.269, G.271, P.272, H.279, W.282, T.283, I.286, F.290, L.318, Q.319, F.322 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.84, B:W.282, B:I.286, B:I.286, B:F.322 Hydrogen bonds: B:T.283, B:Q.319, B:Q.319 pi-Stacking: 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 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.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.6, H2O.8

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.2, H2O.2, H2O.3, H2O.4 MG.7: 2 residues within 4Å: Chain B: D.155 Ligands: MN.6 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.155, H2O.6, H2O.6, H2O.7, H2O.7, H2O.8

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

ACT.4: 9 residues within 4Å: Chain A: I.36, G.37, R.38, K.39, C.40, G.41, R.42, I.43, R.87 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.43 Hydrogen bonds: A:R.38, A:C.40, A:G.41, A:R.42, A:I.43 Water bridges: A:R.87 Salt bridges: A:R.87 ACT.8: 8 residues within 4Å: Chain B: V.33, I.36, K.39, C.40, G.41, R.42, I.43, R.87 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.33, B:I.43 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
D

B
C

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

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