SMTL ID : 6xu0.1

Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: Q.173, K.177, R.394, L.441 Chain B: A.1, T.2, C.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.441, H2O.10 MG.7: 6 residues within 4Å: Chain D: Q.173, K.177, L.441 Chain E: A.1, T.2, C.3 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.441, H2O.18

3 x CAC: CACODYLATE ION(Non-covalent)

CAC.2: 4 residues within 4Å: Chain A: S.334, S.371, Y.374, Y.375 No protein-ligand interaction detected (PLIP) CAC.3: 3 residues within 4Å: Chain A: G.422, G.423, Y.424 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.423 CAC.8: 5 residues within 4Å: Chain D: K.139, G.422, G.423, Y.424, P.425 No protein-ligand interaction detected (PLIP)

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 6 residues within 4Å: Chain A: I.227, S.228, P.229, I.415, P.425, I.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.228 Water bridges: A:I.230 BME.9: 8 residues within 4Å: Chain D: I.227, S.228, P.229, I.230, I.415, P.425, I.426, N.427 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.426

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.241, S.242, K.245, K.246 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.246, A:K.246, A:K.246 Water bridges: A:S.242 GOL.11: 7 residues within 4Å: Chain D: P.56, S.57, L.58, N.61, H.91, I.92, H.93 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:P.56, D:L.58, D:L.58, D:H.93, D:H.93 Water bridges: D:N.61

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.6: 4 residues within 4Å: Chain A: F.312, L.338 Chain D: F.312, Y.325 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.10: 3 residues within 4Å: Chain D: S.150, K.177, W.439 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:W.439, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golovinas, E. et al., Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT. To be published

Release Date

2021-01-27

Peptides

Piwi protein: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

Piwi protein

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