SMTL ID : 7lrc.1

Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.118, H.198, D.199, D.312 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.199, A:D.199, A:D.312, A:D.312 MN.4: 5 residues within 4Å: Chain C: H.118, H.198, D.199, D.312 Ligands: MG.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.199, C:D.199, C:D.312, C:D.312

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.199, E.228 Ligands: MN.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.199 MG.5: 3 residues within 4Å: Chain C: D.199, E.228 Ligands: MN.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.199

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.3: 14 residues within 4Å: Chain A: Y.113, H.114, T.206, L.272, I.313, P.316, H.323, W.326, T.327, I.330, F.334, Q.363, F.366 Chain B: I.562 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.113, A:Y.113, A:T.206, A:W.326, A:I.330, A:I.330, A:F.366, A:F.366, B:I.562 Hydrogen bonds: A:H.323, A:Q.363, A:Q.363 X5M.6: 14 residues within 4Å: Chain C: Y.113, H.114, T.206, L.272, I.313, P.316, H.323, W.326, T.327, I.330, F.334, Q.363, F.366 Chain D: I.562 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.113, C:Y.113, C:T.206, C:W.326, C:I.330, C:I.330, C:F.366, C:F.366, D:I.562 Hydrogen bonds: C:H.323, C:Q.363, C:Q.363

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

2021-06-09

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
C

B
A

D
D

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

Schlafen family member 12

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