SMTL ID : 7eg4.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x J36: Parvine(Covalent)

J36.1: 16 residues within 4Å: Chain A: Y.83, T.176, L.242, I.283, G.285, P.286, H.293, W.296, T.297, I.300, F.304, L.332, Q.333, F.336 Chain B: I.556, I.557 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.242, A:F.304 Hydrogen bonds: A:Q.333 pi-Stacking: A:F.336 J36.5: 16 residues within 4Å: Chain C: Y.83, T.176, L.242, I.283, G.285, P.286, H.293, W.296, T.297, I.300, F.304, L.332, Q.333, F.336 Chain D: I.556, I.557 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.242, C:F.304 Hydrogen bonds: C:Q.333 pi-Stacking: C:F.336

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.88, H.168, D.169, D.282 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.88, A:H.168, A:D.169, A:D.282 MG.3: 2 residues within 4Å: Chain A: D.169, E.198 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain C: H.88, H.168, D.169, D.282 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.88, C:H.168, C:D.169, C:D.282 MG.7: 2 residues within 4Å: Chain C: D.169, E.198 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain B: H.274, F.275, 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: 5 residues within 4Å: Chain D: H.274, F.275, 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

2021-09-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

B
D

D
B

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

Schlafen family member 12

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