SMTL ID : 6qid.1

Crystal structure of DEAH-box ATPase Prp43-S387A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

MPD.1: 7 residues within 4Å: Chain A: R.93, E.163, N.323, E.326, T.399, R.405 Ligands: SO4.21 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.163, A:T.399 Water bridges: A:N.323, A:N.323, A:N.323, A:N.323, A:S.363, A:S.366, A:S.366 MPD.2: 5 residues within 4Å: Chain A: S.490, Y.532, H.533, K.536, R.566 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.536 Hydrogen bonds: A:Y.532, A:K.536, A:R.566 Water bridges: A:Y.532 MPD.3: 3 residues within 4Å: Chain A: R.309, G.311, G.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.311 Water bridges: A:D.279, A:R.309 MPD.4: 5 residues within 4Å: Chain A: T.2, V.10, Y.76, L.79, P.80 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.2, A:V.10, A:Y.76, A:L.79 MPD.5: 7 residues within 4Å: Chain A: P.340, G.341, F.342, P.361, Y.386, E.394, L.395 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.342, A:P.361, A:Y.386, A:L.395 Hydrogen bonds: A:P.340 MPD.7: 5 residues within 4Å: Chain A: R.22, R.26, D.109, V.110, K.111 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.111 Hydrogen bonds: A:V.110 MPD.8: 3 residues within 4Å: Chain A: P.17, W.18, G.20 No protein-ligand interaction detected (PLIP) MPD.9: 3 residues within 4Å: Chain A: Y.400, P.401, D.430 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.400 Hydrogen bonds: A:D.430 Water bridges: A:R.164, A:D.430 MPD.10: 5 residues within 4Å: Chain A: S.284, V.285, Y.286, P.287, R.299 No protein-ligand interaction detected (PLIP) MPD.11: 5 residues within 4Å: Chain A: T.237, Q.240, I.241, E.245, F.383 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.383 Hydrogen bonds: A:Q.240 MPD.12: 4 residues within 4Å: Chain A: E.443, F.602, M.604, Q.605 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.443, A:M.604, A:Q.605 Hydrogen bonds: A:Q.605

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 2 residues within 4Å: Chain A: T.457, P.458 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.451, A:D.451 PEG.13: 6 residues within 4Å: Chain A: A.192, T.193, L.194, A.365, E.397, Q.398 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.397, A:E.397 Water bridges: A:Q.398, A:Q.398

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

CL.14: 2 residues within 4Å: Chain A: G.290, T.322 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: R.93, R.94 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: R.94, R.121, T.136, R.142 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 5 residues within 4Å: Chain A: T.67, D.159, E.160 Ligands: ADP.22, BEF.23 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.67, H2O.4, H2O.5, H2O.8

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

SO4.20: 3 residues within 4Å: Chain A: P.458, L.459, L.462 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.462 SO4.21: 5 residues within 4Å: Chain A: Q.345, K.346, E.402, R.405 Ligands: MPD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.346 Salt bridges: A:R.405

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

ADP.22: 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.19, BEF.23 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.63, A:G.63, A:S.64, A:G.65, A:K.66, A:T.67, A:T.68, A:T.330, A:R.376 Water bridges: A:K.66, A:T.67, A:S.99, A:S.99, A:R.103, A:R.103, A:R.103, A:R.103, A:T.330, A:R.376, A:R.376, 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 BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.23: 10 residues within 4Å: Chain A: T.62, G.63, K.66, E.160, A.192, A.328, R.373, R.376 Ligands: MG.19, ADP.22 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