SMTL ID : 9nyy.1

Nucleic acid bound human SLFN14, State 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

1 x A- U- G- G- G: RNA (5'-R(P*AP*UP*GP*GP*G)-3')(Non-covalent)

A-U-G-G-G.1: 17 residues within 4Å: Chain A: Q.78 Chain B: K.30, K.38, R.39, Q.78, T.82, K.86, R.127, S.137, A.138 Ligands: C-C-C-A-C-U-C.2, C-C-C-A-C-U-C.2, C-C-C-A-C-U-C.2, C-C-C-A-C-U-C.2, C-C-C-A-C-U-C.2, C-C-C-A-C-U-C.2, C-C-C-A-C-U-C.2 Protein-ligand interaction information (PLIP) not available

1 x C- C- C- A- C- U- C: RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')(Non-covalent)

C-C-C-A-C-U-C.2: 16 residues within 4Å: Chain A: K.38, Q.78, T.82, S.137, A.138, K.213, R.214, Y.231, D.249 Ligands: A-U-G-G-G.1, A-U-G-G-G.1, A-U-G-G-G.1, A-U-G-G-G.1, A-U-G-G-G.1, MG.4, MG.5 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.282, C.284, C.318, C.319 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.282, A:C.284, A:C.318, A:C.319 ZN.6: 4 residues within 4Å: Chain B: H.282, C.284, C.318, C.319 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.282, B:C.284, B:C.318, B:C.319

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: T.136, E.206, E.211 Ligands: C-C-C-A-C-U-C.2, C-C-C-A-C-U-C.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.136, A:E.211 MG.5: 5 residues within 4Å: Chain A: E.206, E.211, F.212, K.213 Ligands: C-C-C-A-C-U-C.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:F.212 MG.7: 2 residues within 4Å: Chain B: T.136, E.211 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Riper, J. et al., CryoEM structure of the SLFN14 endoribonuclease reveals insight into RNA binding and cleavage. Nat Commun (2025)

Release Date

2025-07-09

Peptides

Protein SLFN14: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein SLFN14