SMTL ID : 8olj.1

Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: I.54, F.60, K.66, L.75, E.81 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.66, A:K.66, A:E.81, A:E.81 GOL.2: 5 residues within 4Å: Chain A: W.152, L.253, E.254, I.255 Ligands: IPA.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.254, A:E.254 GOL.3: 4 residues within 4Å: Chain A: E.234, E.236, K.237, T.238 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.234, A:E.236, A:T.238, A:T.238, A:T.238 Water bridges: A:S.233 GOL.4: 5 residues within 4Å: Chain A: T.48, I.49, K.50, E.86, D.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.86, A:D.243 GOL.5: 8 residues within 4Å: Chain A: F.60, L.61, P.62, K.66, K.67, R.68, I.73 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.60, A:L.61, A:R.68 Water bridges: A:K.66

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

IPA.6: 5 residues within 4Å: Chain A: N.132, Y.133, S.196, A.199, P.206 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.199, A:P.206 IPA.7: 4 residues within 4Å: Chain A: G.33, L.35, I.255, E.257 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.35, A:L.35, A:I.255, A:E.257 Hydrogen bonds: A:E.257 IPA.8: 2 residues within 4Å: Chain A: Y.36, N.220 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.219, A:N.220 IPA.9: 3 residues within 4Å: Chain A: V.51, Y.74, D.85 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.51, A:Y.74 IPA.10: 6 residues within 4Å: Chain A: N.38, V.161, D.162, L.163, L.222 Ligands: ACY.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.222 Hydrogen bonds: A:L.163, A:L.163 Water bridges: A:D.162 IPA.11: 4 residues within 4Å: Chain A: V.43, N.44, Y.45, E.47 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.45, A:Y.45, A:E.47 Hydrogen bonds: A:N.44, A:Y.45 IPA.12: 4 residues within 4Å: Chain A: I.39, H.150, W.152 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.39, A:W.152 IPA.13: 2 residues within 4Å: Chain A: Y.78, E.108 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.78, A:Y.78 Hydrogen bonds: A:E.108 IPA.14: 5 residues within 4Å: Chain A: Y.78, I.105, E.108, N.109, S.240 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.78, A:E.108 Hydrogen bonds: A:N.109, A:S.240 Water bridges: A:N.109, A:S.240

3 x K: POTASSIUM ION(Non-covalent)

K.15: 2 residues within 4Å: Chain A: K.251, P.252 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:P.252, H2O.5, H2O.5, H2O.8 K.16: 2 residues within 4Å: Chain A: E.131, Y.143 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.131, A:Y.143, H2O.4, H2O.7 K.17: 2 residues within 4Å: Chain A: S.136, N.137 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.136, A:S.136, H2O.1

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.18: 4 residues within 4Å: Chain A: Y.178, K.190, K.191, W.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.190, A:K.190

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.19: 2 residues within 4Å: Chain A: F.219 Ligands: IPA.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manakova, E. et al., The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res. (2024)

Release Date

2024-01-24

Peptides

Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains

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