SMTL ID : 6cbd.1

Crystal Structure of Human Argonaute2 Bound to Three Tryptophans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 6 residues within 4Å: Chain A: L.650, Y.654, K.660, L.694, E.695, Y.698 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:Y.654, A:K.660, A:L.694 Hydrogen bonds: A:K.660, A:E.695 pi-Stacking: A:Y.698 TRP.2: 9 residues within 4Å: Chain A: F.587, Q.588, 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 TRP.3: 8 residues within 4Å: Chain A: R.688, C.691, I.692, Y.698, Q.699, P.700, I.702, D.771 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:R.688, A:I.692, A:Q.699, A:Q.699 Hydrogen bonds: A:Q.699, A:P.700

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

IPA.4: 4 residues within 4Å: Chain A: A.184, E.197, A.227, A.348 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.227, A:A.348 Hydrogen bonds: A:E.197 IPA.5: 6 residues within 4Å: Chain A: T.599, H.600, P.601, P.602 Chain B: G.9, C.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.602 Hydrogen bonds: A:T.599, A:T.599 Water bridges: A:R.814 IPA.7: 5 residues within 4Å: Chain A: K.525, Q.548 Chain B: U.1 Chain C: A.2, A.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.525

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

MG.6: 4 residues within 4Å: Chain A: D.597, V.598, D.669 Chain B: C.10 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.597, A:V.598, H2O.1, H2O.2, H2O.6, H2O.10 MG.8: 2 residues within 4Å: Chain B: C.12, A.13 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain C: U.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheu-Gruttadauria, J. et al., Phase Transitions in the Assembly and Function of Human miRISC. Cell (2018)

Release Date

2018-04-18

Peptides

Protein argonaute-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein argonaute-2

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