SMTL ID : 7eg1.1

Cryo-EM structure of DNMDP-induced PDE3A-SLFN12 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

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: 19 residues within 4Å: Chain A: Y.83, H.84, T.176, L.242, I.283, N.284, G.285, P.286, H.293, W.296, T.297, I.300, F.304, L.332, Q.333, F.336 Chain B: L.553, I.556, I.557 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.176, A:W.296, A:I.300, A:F.336, B:L.553, B:I.556, B:I.557 Hydrogen bonds: A:Q.333, A:Q.333 pi-Stacking: A:F.336 X5M.5: 19 residues within 4Å: Chain C: Y.83, H.84, T.176, L.242, I.283, N.284, G.285, P.286, H.293, W.296, T.297, I.300, F.304, L.332, Q.333, F.336 Chain D: L.553, I.556, I.557 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:T.176, C:W.296, C:I.300, D:L.553, D:I.556, D:I.557 Hydrogen bonds: C:Q.333, C:Q.333 pi-Stacking: C:F.336

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.88, H.168, D.169, D.282 Ligands: MG.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.88, A:H.168, A:D.169, A:D.282 MG.3: 3 residues within 4Å: Chain A: D.169, E.198 Ligands: MG.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.169 MG.6: 5 residues within 4Å: Chain C: H.88, H.168, D.169, D.282 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.88, C:H.168, C:D.169, C:D.282 MG.7: 3 residues within 4Å: Chain C: D.169, E.198 Ligands: MG.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.169

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: H.274, C.276, C.310, C.311 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.274, B:C.276, B:C.310, B:C.311 ZN.8: 4 residues within 4Å: Chain D: H.274, C.276, C.310, C.311 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.274, D:C.276, D:C.310, D:C.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nat Commun (2021)

Release Date

2021-11-03

Peptides

cGMP-inhibited 3',5'-cyclic phosphodiesterase A: AC
Schlafen family member 12: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

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

Schlafen family member 12

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