SMTL ID : 4tyw.1

DEAD-box helicase Mss116 bound to ssRNA and ADP-BeF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x A- A- A- A- A- A- A: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')(Non-covalent)

A-A-A-A-A-A-A.1: 31 residues within 4Å: Chain A: P.102, T.103, R.104, V.133, G.134, G.135, T.136, T.156, P.157, G.158, R.159, D.162, R.185, G.190, F.191, P.295, T.296, V.297, K.298, H.321, G.322, R.329, T.347, D.348, V.349, S.369, I.445, S.446, S.449, S.450, S.453 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: K.72, T.73, D.181, E.182, G.353 Ligands: BEF.4, ADP.5 No protein-ligand interaction detected (PLIP) MG.3: 7 residues within 4Å: Chain A: F.356, P.357, N.358, V.359, R.380, T.381, R.383 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.356, A:R.380, H2O.3

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.4: 10 residues within 4Å: Chain A: T.68, G.69, K.72, E.182, A.220, G.353, R.380, R.383 Ligands: MG.2, ADP.5 No protein-ligand interaction detected (PLIP)

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

ADP.5: 21 residues within 4Å: Chain A: F.40, P.41, G.42, L.43, T.44, Q.47, K.67, T.68, G.69, T.70, G.71, K.72, T.73, F.74, E.113, K.116, D.355, R.383, S.384 Ligands: MG.2, BEF.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.42, A:T.44, A:Q.47, A:G.69, A:T.70, A:T.70, A:G.71, A:K.72, A:T.73, A:T.73, A:T.73 Water bridges: A:F.74, A:Q.109, A:Q.109, A:D.181, A:D.355, A:D.355, A:R.383 Salt bridges: A:K.72, A:R.383, A:R.383 pi-Stacking: A:F.40, A:F.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mallam, A.L. et al., Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase. Elife (2014)

Release Date

2014-12-31

Peptides

ATP-dependent RNA helicase MSS116, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent RNA helicase MSS116, mitochondrial