SMTL ID : 9bez.1

MID domain of human Argo2 bound to RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x 01: [(3~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate

01.1: 9 residues within 4Å: Chain A: L.83, Y.90, K.94, T.105, Q.106, C.107, Q.109, K.127, K.131 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.90 Hydrogen bonds: A:Y.90, A:Q.106, A:C.107, A:Q.109 Salt bridges: A:K.94, A:K.94, A:K.127, A:K.131, A:K.131 pi-Stacking: A:Y.90 01.2: 10 residues within 4Å: Chain B: G.85, K.86, Y.90, K.94, T.105, Q.106, C.107, Q.109, K.127, K.131 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Q.109 Hydrogen bonds: B:Y.90, B:Q.106, B:C.107, B:K.127 Salt bridges: B:K.94, B:K.94, B:K.127, B:K.131, B:K.131 01.3: 11 residues within 4Å: Chain C: L.83, K.86, T.87, Y.90, K.94, D.98, Q.106, C.107, Q.109, K.127, K.131 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.90 Hydrogen bonds: C:G.85, C:T.87, C:Y.90, C:Q.106 Water bridges: C:K.127, C:K.131 Salt bridges: C:K.94, C:K.127, C:K.127, C:K.131, C:K.131, C:K.131 pi-Stacking: C:Y.90 pi-Cation interactions: C:K.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, L. et al., Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His 6 -SUMO Tag Removal, Nucleotide Binding, and Crystal Growth. Curr Protoc (2024)

Release Date

2024-07-10

Peptides

Protein argonaute-2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Protein argonaute-2

Related Entries With Identical Sequence