SMTL ID : 6c90.1

Human Mtr4 helicase in complex with ZCCHC8-CTD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 13 residues within 4Å: Chain A: F.71, I.72, L.73, D.74, Q.77, T.96, S.97, G.99, K.100, T.101, V.102, N.423, R.460 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.74, A:Q.77, A:Q.77, A:S.97, A:G.99, A:K.100, A:T.101, A:T.101, A:R.460 Water bridges: A:T.101, A:K.131, A:R.460, A:R.460 Salt bridges: A:K.100 pi-Stacking: A:F.71, A:F.71 pi-Cation interactions: A:R.460, A:R.460

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.488 Ligands: TLA.8 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: L.506, L.507, V.509, I.512 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.506, A:L.507, A:V.509, A:I.512, H2O.7, H2O.8

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 3 residues within 4Å: Chain A: R.546, E.644, Y.650 7 PLIP interactions: 7 interactions with chain A Water bridges: A:L.498, A:Y.500, A:R.546, A:S.638, A:E.644 Salt bridges: A:R.546, A:R.546 MLI.5: 5 residues within 4Å: Chain A: I.124, K.125, A.126, R.195, R.691 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.124, A:K.125 Hydrogen bonds: A:K.125, A:A.126 Salt bridges: A:K.125, A:K.125, A:R.195, A:R.691 MLI.6: 6 residues within 4Å: Chain A: F.327, K.329, H.389, G.390, T.415, T.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.390, A:T.415 Salt bridges: A:K.329, A:K.329 MLI.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.8: 6 residues within 4Å: Chain A: E.46, I.219, P.220, A.222, Y.241 Ligands: MG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.222 Salt bridges: A:R.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Puno, M.R. et al., Structural basis for MTR4-ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-05-30

Peptides

Exosome RNA helicase MTR4,Exosome RNA helicase MTR4: A
Zinc finger CCHC domain-containing protein 8: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exosome RNA helicase MTR4,Exosome RNA helicase MTR4

Zinc finger CCHC domain-containing protein 8