SMTL ID : 5js2.1

Human Argonaute-2 Bound to a Modified siRNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

monomer

Ligands

1 x 6OP- F2T- 6NW- UFT- 6OO- UFT: modified siRNA(Non-covalent)

6OP-F2T-6NW-UFT-6OO-UFT.1: 29 residues within 4Å: Chain A: L.522, G.524, K.525, T.526, Y.529, K.533, T.544, Q.545, C.546, V.547, Q.548, N.551, T.559, N.562, L.563, K.566, K.570, K.709, H.753, R.761, Y.790, R.792, C.793, R.795, V.797, S.798, Y.804, R.812, Y.815 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.562, A:G.524, A:T.526, A:K.533, A:Q.545, A:C.546, A:Q.548, A:K.566, A:K.570, A:K.570, A:R.812, A:Q.548, A:N.562, A:K.566 Water bridges: A:Q.757, A:R.761 Hydrophobic interactions: A:Y.529, A:Y.529, A:Y.529 Salt bridges: A:K.709

2 x IPH: PHENOL(Non-covalent)

IPH.2: 7 residues within 4Å: Chain A: L.650, I.651, Y.654, K.660, L.694, E.695, Y.698 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.650, A:I.651, A:Y.654, A:K.660, A:K.660, A:L.694 Hydrogen bonds: A:E.695 pi-Stacking: A:Y.698 IPH.3: 8 residues within 4Å: Chain A: F.587, Q.589, P.590, V.591, D.619, A.620, F.653, F.659 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.591, A:A.620, A:F.653, A:F.659 Hydrogen bonds: A:F.587

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: G.178, R.179, S.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.177, A:R.179 Salt bridges: A:R.179

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: D.597, V.598 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.597, A:D.597, A:V.598

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schirle, N.T. et al., Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide. J.Am.Chem.Soc. (2016)

Release Date

2016-07-20

Peptides

Protein argonaute-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein argonaute-2

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