SMTL ID : 4w5o.1

The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: D.597, V.598 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.597, A:V.598, H2O.3, H2O.3, H2O.3, H2O.14 MG.8: 1 residues within 4Å: Chain B: A.13 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain C: U.4 No protein-ligand interaction detected (PLIP)

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 6 residues within 4Å: Chain A: A.184, E.197, W.199, K.226, A.227, A.348 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.199, A:A.348 IPA.3: 5 residues within 4Å: Chain A: P.580, Q.581, R.583, P.584, F.587 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.587 Hydrogen bonds: A:Q.581, A:R.583

4 x IPH: PHENOL(Non-covalent)

IPH.4: 8 residues within 4Å: Chain A: R.688, C.691, I.692, Y.698, Q.699, P.700, I.702, D.771 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.688, A:R.688, A:I.692, A:Q.699 Hydrogen bonds: A:P.700 IPH.5: 5 residues within 4Å: Chain A: L.650, Y.654, K.660, E.695, Y.698 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.654, A:K.660 pi-Stacking: A:Y.698 IPH.6: 7 residues within 4Å: Chain A: F.587, Q.589, P.590, V.591, A.620, F.653, F.659 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.590, A:V.591, A:A.620, A:F.653, A:F.659 Hydrogen bonds: A:F.587 IPH.7: 8 residues within 4Å: Chain A: G.536, G.541, M.542, A.543, K.570, T.852, T.855, Y.857 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.543, A:T.852, A:T.855, A:Y.857 Hydrogen bonds: A:K.570

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

PO4.9: 2 residues within 4Å: Chain A: Q.332 Chain B: U.18 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schirle, N.T. et al., Gene regulation. Structural basis for microRNA targeting. Science (2014)

Release Date

2014-11-12

Peptides

Protein argonaute-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein argonaute-2

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