SMTL ID : 7lrd.1

Cryo-EM of the SLFN12-PDE3A complex: Consensus subset model

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.280, C.282, C.316, C.317 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.280, A:C.282, A:C.316, A:C.317 ZN.5: 4 residues within 4Å: Chain C: H.280, C.282, C.316, C.317 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.280, C:C.282, C:C.316, C:C.317

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

MN.2: 5 residues within 4Å: Chain B: H.118, H.198, D.199, D.312 Ligands: MG.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.199, B:D.199, B:D.312, B:D.312 MN.6: 5 residues within 4Å: Chain D: H.118, H.198, D.199, D.312 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.199, D:D.199, D:D.312, D:D.312

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: D.199, E.228 Ligands: MN.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.199 MG.7: 3 residues within 4Å: Chain D: D.199, E.228 Ligands: MN.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D: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.4: 14 residues within 4Å: Chain A: I.562 Chain B: 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 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.113, B:Y.113, B:T.206, B:W.326, B:I.330, B:I.330, B:F.366, B:F.366, A:I.562 Hydrogen bonds: B:H.323, B:Q.363, B:Q.363 X5M.8: 14 residues within 4Å: Chain C: I.562 Chain D: 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 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.113, D:Y.113, D:T.206, D:W.326, D:I.330, D:I.330, D:F.366, D:F.366, C:I.562 Hydrogen bonds: D:H.323, D:Q.363, D: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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Schlafen family member 12

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

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