SMTL ID : 6t5t.1

Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTGGCCACAAT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: Q.173, K.177, L.441 Chain B: A.1, T.2, T.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.441, H2O.12 MG.2: 5 residues within 4Å: Chain A: S.234, E.235, Y.236, L.237, T.238 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: E.372, E.373, Y.374, Y.375, H.376 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.372, H2O.5 MG.14: 6 residues within 4Å: Chain D: Q.173, K.177, L.441 Chain E: A.1, T.2, T.3 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.441, H2O.24 MG.15: 5 residues within 4Å: Chain D: S.234, E.235, Y.236, L.237, T.238 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain D: E.372, E.373, Y.374, Y.375, H.376 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.372, H2O.17

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: W.313 Chain D: K.331 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: K.331 Chain D: W.313 Ligand excluded by PLIP

6 x K: POTASSIUM ION(Non-covalent)

K.5: 2 residues within 4Å: Chain A: S.57, L.58 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.57, A:L.58, H2O.5 K.6: 2 residues within 4Å: Chain A: T.120, G.121 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.121, H2O.4, H2O.10, H2O.11 K.7: 5 residues within 4Å: Chain A: L.332, R.336, Y.337, S.361, V.362 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.337, A:S.361, H2O.5 K.18: 2 residues within 4Å: Chain D: S.57, L.58 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.57, D:L.58, H2O.18 K.19: 2 residues within 4Å: Chain D: T.120, G.121 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:G.121, H2O.17, H2O.22, H2O.23 K.20: 5 residues within 4Å: Chain D: L.332, R.336, Y.337, S.361, V.362 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.337, D:S.361, H2O.18

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

BME.8: 6 residues within 4Å: Chain A: G.220, T.221, M.222, M.391, W.393, Y.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.222 Water bridges: A:M.222 BME.9: 7 residues within 4Å: Chain A: I.227, S.228, P.229, I.230, I.415, P.425, I.426 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.426 BME.10: 3 residues within 4Å: Chain A: I.230, V.231, Y.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.239 BME.11: 3 residues within 4Å: Chain A: F.312 Chain D: F.312 Ligands: BME.24 No protein-ligand interaction detected (PLIP) BME.12: 5 residues within 4Å: Chain A: G.327, K.329, D.383, Y.386, Y.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.329 BME.13: 6 residues within 4Å: Chain A: V.187, K.191, G.192, K.218, E.384, Y.387 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.188 BME.21: 6 residues within 4Å: Chain D: G.220, T.221, M.222, M.391, W.393, Y.407 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.222 Water bridges: D:M.222 BME.22: 7 residues within 4Å: Chain D: I.227, S.228, P.229, I.230, I.415, P.425, I.426 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.426 BME.23: 3 residues within 4Å: Chain D: I.230, V.231, Y.239 No protein-ligand interaction detected (PLIP) BME.24: 3 residues within 4Å: Chain A: F.312 Chain D: F.312 Ligands: BME.11 No protein-ligand interaction detected (PLIP) BME.25: 5 residues within 4Å: Chain D: G.327, K.329, D.383, Y.386, Y.387 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.329, D:D.383 BME.26: 6 residues within 4Å: Chain D: V.187, K.191, G.192, K.218, E.384, Y.387 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golovinas, E. et al., Crystal structure of Archaeoglobus fulgidusArgonaute protein with cognate DNA oligoduplex 5'-pATTGTGGCCACAAT. To be published

Release Date

2020-11-18

Peptides

Piwi protein AF_1318: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

Piwi protein AF_1318

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