SMTL ID : 9bf0.1

MID domain of human Argo2 bound to UTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-trimer

Ligands

3 x UTP: URIDINE 5'-TRIPHOSPHATE(Covalent)(Non-covalent)

UTP.1: 12 residues within 4Å: Chain A: L.81, G.83, K.84, T.85, Y.88, K.92, T.103, Q.104, C.105, Q.107, K.125, K.129 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.88 Hydrogen bonds: A:G.83, A:T.85, A:Y.88, A:T.103, A:Q.104, A:C.105, A:Q.107 Water bridges: A:Y.88, A:Q.107 Salt bridges: A:K.92, A:K.92, A:K.125, A:K.125, A:K.129, A:K.129 UTP.2: 12 residues within 4Å: Chain B: L.81, G.83, K.84, T.85, Y.88, K.92, T.103, Q.104, C.105, Q.107, K.125, K.129 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.88 Hydrogen bonds: B:G.83, B:K.84, B:K.84, B:T.85, B:Y.88, B:Y.88, B:T.103, B:Q.104, B:C.105 Water bridges: B:Q.107, B:K.125, B:K.125, B:K.129 Salt bridges: B:K.92, B:K.92, B:K.92, B:K.125, B:K.125, B:K.125, B:K.129, B:K.129, B:K.129 pi-Cation interactions: B:K.84 UTP.3: 11 residues within 4Å: Chain C: L.81, G.83, K.84, T.85, Y.88, K.92, T.103, Q.104, C.105, Q.107, K.129 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.88 Hydrogen bonds: C:G.83, C:T.85, C:Y.88, C:T.103, C:Q.104, C:C.105, C:Q.107 Water bridges: C:K.84, C:Q.107, C:K.129, C:K.129, C:K.129 Salt bridges: C:K.92, C:K.92, C:K.129, C:K.129

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