SMTL ID : 6ra4.1

Human ARGONAUTE-2 PAZ DOMAIN (214-347) IN COMPLEX WITH CGUGACUCU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x C- G- U- G- A- C- U- C- U: RNA (5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3')(Non-covalent)

C-G-U-G-A-C-U-C-U.1: 29 residues within 4Å: Chain A: K.47, H.52, M.56, R.58, Y.60, R.61, F.75, L.77, V.89, Y.92, F.93, R.96, H.97, Q.113, K.116, H.117, T.118, Y.119 Chain B: Q.55, M.56, K.57, R.58 Ligands: C-G-U-G-A-C-U-C-U.2, C-G-U-G-A-C-U-C-U.2, C-G-U-G-A-C-U-C-U.2, C-G-U-G-A-C-U-C-U.2, C-G-U-G-A-C-U-C-U.2, C-G-U-G-A-C-U-C-U.2, GOL.3 Protein-ligand interaction information (PLIP) not available C-G-U-G-A-C-U-C-U.2: 30 residues within 4Å: Chain A: Q.55, M.56, K.57, R.58 Chain B: F.5, K.47, H.52, M.56, R.58, Y.60, R.61, F.75, L.77, Y.92, F.93, R.96, H.97, K.116, H.117, T.118, Y.119, L.120, G.130 Ligands: C-G-U-G-A-C-U-C-U.1, C-G-U-G-A-C-U-C-U.1, C-G-U-G-A-C-U-C-U.1, C-G-U-G-A-C-U-C-U.1, C-G-U-G-A-C-U-C-U.1, C-G-U-G-A-C-U-C-U.1, GOL.4 Protein-ligand interaction information (PLIP) not available

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: K.59 Ligands: C-G-U-G-A-C-U-C-U.1 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain B: K.47, K.59, Y.60, R.61 Ligands: C-G-U-G-A-C-U-C-U.2, C-G-U-G-A-C-U-C-U.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.61 Water bridges: B:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Greenidge, P.A. et al., How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection. J.Chem.Inf.Model. (2019)

Release Date

2019-05-08

Peptides

Protein argonaute-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein argonaute-2