SMTL ID : 6qie.1

Crystal structure of DEAH-box ATPase Prp43-S387G

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 3 residues within 4Å: Chain A: Y.532, K.536, R.566 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.532, A:K.536 Hydrogen bonds: A:R.566 MPD.2: 5 residues within 4Å: Chain A: T.2, V.10, Y.76, L.79, P.80 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.2, A:V.10, A:Y.76, A:L.79, A:P.80 MPD.3: 5 residues within 4Å: Chain A: R.353, E.443, G.601, M.604, Q.605 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.443, A:Q.605 MPD.4: 4 residues within 4Å: Chain A: D.279, R.309, G.311, R.313 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.313 Hydrogen bonds: A:R.309, A:R.309 MPD.5: 5 residues within 4Å: Chain A: G.341, F.342, Y.386, E.394, L.395 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.342, A:Y.386, A:L.395 Hydrogen bonds: A:E.227 MPD.6: 2 residues within 4Å: Chain A: P.17, W.18 No protein-ligand interaction detected (PLIP) MPD.7: 3 residues within 4Å: Chain A: K.198, P.401, D.430 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.430 MPD.8: 5 residues within 4Å: Chain A: R.121, S.464, E.465, F.466, P.467 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.467 Hydrogen bonds: A:R.121, A:R.121 MPD.9: 3 residues within 4Å: Chain A: N.589, N.593, R.596 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.596

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

ADP.10: 15 residues within 4Å: Chain A: L.37, E.61, T.62, G.63, S.64, G.65, K.66, T.67, T.68, R.103, T.330, R.376, T.377 Ligands: MG.17, BEF.18 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.61, A:G.63, A:G.63, A:S.64, A:G.65, A:K.66, A:T.67, A:T.67, A:T.67, A:T.68, A:T.330, A:R.376 Water bridges: A:T.67, A:D.159, A:R.376, A:R.376 Salt bridges: A:K.66, A:R.376, A:R.376 pi-Cation interactions: A:R.103, A:R.103

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain A: K.346, R.405 Ligand excluded by PLIP

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 1 residues within 4Å: Chain A: P.458 No protein-ligand interaction detected (PLIP) SO4.13: 5 residues within 4Å: Chain A: R.94, I.120, R.121, T.136, R.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.94, A:R.121 Salt bridges: A:R.142 SO4.14: 2 residues within 4Å: Chain A: R.93, R.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 SO4.15: 4 residues within 4Å: Chain A: Q.177, V.420, E.421, D.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.177, A:E.421, A:D.422, A:D.422 SO4.16: 3 residues within 4Å: Chain A: S.24, E.25, R.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.25, A:R.26

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 5 residues within 4Å: Chain A: T.67, D.159, E.160 Ligands: ADP.10, BEF.18 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.67, A:E.160, H2O.1, H2O.1, H2O.1

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

BEF.18: 9 residues within 4Å: Chain A: T.62, G.63, K.66, E.160, A.192, R.373, R.376 Ligands: ADP.10, MG.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamann, F. et al., Structural basis for RNA translocation by DEAH-box ATPases. Nucleic Acids Res. (2019)

Release Date

2019-03-06

Peptides

Prp43: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Prp43