SMTL ID : 6kr6.1

Crystal structure of Drosophila Piwi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x U- A- U- U- N: piRNA(Non-covalent)

U-A-U-U-N.1: 25 residues within 4Å: Chain A: N.512, D.513, N.514, A.515, Y.518, K.522, T.533, Q.534, V.535, V.536, T.537, T.540, I.549, K.552, I.553, Q.556, K.560, Y.768, N.770, W.771, Q.782, K.785, K.786, L.810 Ligands: ZN.2 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: Q.556, L.810 Ligands: U-A-U-U-N.1, U-A-U-U-N.1, U-A-U-U-N.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.810 ZN.3: 2 residues within 4Å: Chain A: H.211, D.716 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.211 ZN.4: 2 residues within 4Å: Chain A: N.794, H.796 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.796 ZN.11: 3 residues within 4Å: Chain A: H.83, H.85, Q.119 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.83, A:H.85 ZN.12: 1 residues within 4Å: Chain A: H.413 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.413 ZN.13: 2 residues within 4Å: Chain A: D.581, D.652 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.581, A:D.581, A:D.652 ZN.14: 3 residues within 4Å: Chain A: D.440, D.443, K.504 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.440, A:D.440, A:D.443 ZN.15: 1 residues within 4Å: Chain A: H.455 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.455

6 x HG: MERCURY (II) ION(Non-covalent)

HG.5: 2 residues within 4Å: Chain A: C.284, R.287 No protein-ligand interaction detected (PLIP) HG.6: 4 residues within 4Å: Chain A: D.652, V.777, C.781, Q.782 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.652, A:C.781 HG.7: 5 residues within 4Å: Chain A: A.446, Q.479, C.498, S.501, P.503 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.498, A:S.501 HG.8: 2 residues within 4Å: Chain A: C.615, T.624 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.615 HG.9: 2 residues within 4Å: Chain A: C.155, Q.210 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.155, A:C.155 HG.10: 2 residues within 4Å: Chain A: C.238, E.248 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamaguchi, S. et al., Crystal structure of Drosophila Piwi. Nat Commun (2020)

Release Date

2020-02-19

Peptides

Protein piwi: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein piwi