SMTL ID : 5d0u.1

Crystal structure of the RNA-helicase Prp43 from Chaetomium thermophilum bound to ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

monomer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: L.38, T.63, G.64, S.65, G.66, K.67, T.68, T.69, S.100, R.104, F.302, T.331, D.333, R.377 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.62, A:G.64, A:G.64, A:S.65, A:G.66, A:K.67, A:T.68, A:T.69, A:S.100, A:T.331, A:D.333, A:R.377 Water bridges: A:K.67, A:K.67, A:T.68, A:Q.92 Salt bridges: A:K.67 pi-Stacking: A:F.302

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.68, D.160, E.161, S.329 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.68, H2O.1, H2O.1, H2O.1, H2O.1

9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: D.523, R.596, Y.639, R.662 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.596, A:R.596 Salt bridges: A:D.523 pi-Cation interactions: A:Y.639 DMS.4: 3 residues within 4Å: Chain A: I.629, V.635, P.638 No protein-ligand interaction detected (PLIP) DMS.5: 6 residues within 4Å: Chain A: R.354, E.444, A.472, G.602, M.605, Q.606 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.444 DMS.6: 4 residues within 4Å: Chain A: L.626, L.628, K.652, Q.653 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.653 DMS.7: 10 residues within 4Å: Chain A: L.495, L.496, V.498, P.499, Q.500, L.529, N.645, E.646, T.657 Ligands: DMS.9 No protein-ligand interaction detected (PLIP) DMS.8: 4 residues within 4Å: Chain A: L.555, S.556, Y.557, R.558 No protein-ligand interaction detected (PLIP) DMS.9: 7 residues within 4Å: Chain A: W.502, K.516, D.525, S.632, R.656, T.657 Ligands: DMS.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.657 Salt bridges: A:D.525 DMS.10: 6 residues within 4Å: Chain A: P.341, G.342, F.343, P.362, Y.387, E.395 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.395 DMS.11: 7 residues within 4Å: Chain A: Y.447, F.604, I.669, A.670, P.671, V.672, Y.673 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.604

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tauchert, M.J. et al., Structural and functional analysis of the RNA helicase Prp43 from the thermophilic eukaryote Chaetomium thermophilum. Acta Crystallogr.,Sect.F (2016)

Release Date

2016-02-10

Peptides

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43

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