SMTL ID : 8ok9.1

Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: Q.173, K.177, L.441 Chain C: A.1, C.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.441

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

ACY.2: 4 residues within 4Å: Chain A: K.139, G.422, G.423, Y.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.423 Salt bridges: A:K.139 ACY.3: 8 residues within 4Å: Chain A: D.13, P.14, E.17, K.329, K.331, Y.337, H.379 Chain B: V.258 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.331, A:Y.337 Hydrogen bonds: A:D.13 Salt bridges: A:H.379 ACY.4: 2 residues within 4Å: Chain A: R.420, Y.421 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.420, A:Y.421 ACY.5: 1 residues within 4Å: Chain A: Y.325 No protein-ligand interaction detected (PLIP) ACY.6: 4 residues within 4Å: Chain A: P.311, F.312, R.336 Chain B: N.148 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.336, B:V.149 Salt bridges: A:R.336 ACY.10: 7 residues within 4Å: Chain B: S.52, L.75, G.79, I.80, E.81, N.82, E.83 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.83 Hydrogen bonds: B:E.81, B:E.81, B:N.82, B:E.83, B:E.83 ACY.11: 1 residues within 4Å: Chain B: E.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.58 ACY.14: 4 residues within 4Å: Chain A: R.48 Chain D: C.7, A.8, G.15 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.48

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 2 residues within 4Å: Chain A: E.42, K.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.42, A:K.45 EDO.8: 3 residues within 4Å: Chain A: T.370, S.371, E.372 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.371, A:E.372 EDO.9: 6 residues within 4Å: Chain A: K.262, L.263, K.300, W.369, N.377, I.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.263, A:K.300 EDO.12: 3 residues within 4Å: Chain A: M.315 Chain B: Y.36, P.252 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain B: W.194 Chain D: T.2, C.3 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain D: A.1, T.2 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 6 residues within 4Å: Chain A: P.318, R.321, F.322 Chain B: A.212, T.213, R.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:R.321 Water bridges: A:P.318

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

Piwi protein AF_1318: A
Archaeoglobus fulgidus AfAgo-N protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Piwi protein AF_1318

Archaeoglobus fulgidus AfAgo-N protein

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