SMTL ID : 8wzc.1

NYN domain of human KHNYN complex with RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x U- U- U- A- U: RNA (5'-R(P*UP*UP*UP*AP*U)-3')

U-U-U-A-U.1: 16 residues within 4Å: Chain A: D.11, S.13, N.14, M.17, Q.22, W.52, A.58, R.87, Y.91, D.93, N.110, D.111, Q.112, R.114 Ligands: MG.5, MG.6 Protein-ligand interaction information (PLIP) not available

3 x GOL: GLYCEROL

GOL.2: 7 residues within 4Å: Chain A: H.7, R.43, D.44, I.45, T.46, S.73, L.74 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.44, A:D.44, A:I.45 Water bridges: A:I.45, A:S.73, A:S.76 GOL.3: 4 residues within 4Å: Chain A: M.142, V.143, P.144, D.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.145 GOL.4: 3 residues within 4Å: Chain A: V.34, Q.35, W.38 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.31, A:Q.35

2 x MG: MAGNESIUM ION

MG.5: 5 residues within 4Å: Chain A: Y.91, D.93, D.111 Ligands: U-U-U-A-U.1, U-U-U-A-U.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.93, A:D.111, H2O.1, H2O.7 MG.6: 4 residues within 4Å: Chain A: D.92, D.93 Ligands: U-U-U-A-U.1, U-U-U-A-U.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.92, A:D.93, H2O.1, H2O.1, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, S. et al., Crystal structure of NYN domain of Human KHNYN in complex with single strand RNA. Biochem.Biophys.Res.Commun. (2024)

Release Date

2024-09-11

Peptides

Protein KHNYN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein KHNYN