SMTL ID : 9bf2.1

MID domain of Ago2 bound to UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-trimer

Ligands

3 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U.1: 12 residues within 4Å: Chain A: L.83, G.85, K.86, T.87, Y.90, K.94, T.105, Q.106, C.107, Q.109, K.127, K.131 46 PLIP interactions: 14 interactions with chain B, 17 interactions with chain C, 15 interactions with chain A Hydrophobic interactions: B:Y.90, C:Y.90, A:Y.90 Hydrogen bonds: B:G.85, B:T.87, B:Y.90, B:T.105, B:Q.106, B:C.107, C:G.85, C:T.87, C:Y.90, C:T.105, C:Q.106, C:C.107, C:Q.109, C:K.127, A:G.85, A:K.86, A:T.87, A:T.105, A:Q.106, A:C.107, A:K.127 Water bridges: B:Y.90, B:Q.109, B:K.111, B:K.131, C:Y.90, C:K.94, C:Q.109, C:K.127, C:K.127, C:K.127, A:Q.109, A:K.127, A:K.127, A:K.131 Salt bridges: B:K.94, B:K.131, C:K.94, C:K.131, A:K.94, A:K.131 pi-Cation interactions: B:K.86, A:K.86 U.2: 11 residues within 4Å: Chain B: L.83, G.85, K.86, T.87, Y.90, K.94, T.105, Q.106, C.107, Q.109, K.131 Protein-ligand interaction information (PLIP) not available U.3: 12 residues within 4Å: Chain C: L.83, G.85, K.86, T.87, Y.90, K.94, T.105, Q.106, C.107, Q.109, K.127, K.131 Protein-ligand interaction information (PLIP) not available

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

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