SMTL ID : 5ltj.1

Crystal structure of the Prp43-ADP-BeF3 complex (in orthorhombic space group)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: L.38, E.62, T.63, G.64, S.65, G.66, K.67, T.68, T.69, R.104, T.331, R.377, T.378 Ligands: BEF.2, MG.3 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:G.64, A:G.64, A:S.65, A:G.66, A:K.67, A:T.68, A:T.68, A:T.69, A:T.331, A:R.377 Water bridges: A:K.67, A:T.68, A:T.68, A:S.100, A:S.100, A:R.104, A:R.104, A:R.104, A:R.104, A:T.331, A:D.333, A:R.377, A:R.377, A:R.377 Salt bridges: A:K.67, A:R.377, A:R.377 pi-Cation interactions: A:R.104, A:R.104

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

BEF.2: 10 residues within 4Å: Chain A: T.63, G.64, K.67, E.161, A.193, S.329, R.374, R.377 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.68, D.160, E.161 Ligands: ADP.1, BEF.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.68, H2O.1, H2O.3, H2O.6

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

MPD.4: 7 residues within 4Å: Chain A: P.341, G.342, F.343, P.362, Y.387, A.391, E.395 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.343, A:P.362, A:Y.387, A:Y.387, A:A.391 Water bridges: A:L.386, A:L.386 MPD.5: 8 residues within 4Å: Chain A: R.94, E.164, N.324, E.327, S.367, T.400, R.406 Ligands: SO4.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.400 Water bridges: A:N.324, A:N.324, A:S.364, A:S.367, A:S.367, A:S.367, A:T.400, A:T.400 MPD.6: 4 residues within 4Å: Chain A: Y.533, H.534, K.537, R.567 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.537, A:K.537 MPD.7: 3 residues within 4Å: Chain A: R.310, G.312, G.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.312 MPD.8: 5 residues within 4Å: Chain A: L.626, V.627, L.628, K.652, Q.653 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.628, A:L.628, A:Q.653 Hydrogen bonds: A:Q.653 MPD.9: 6 residues within 4Å: Chain A: E.444, A.472, F.603, M.605, Q.606, K.622 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.472, A:F.603, A:M.605, A:Q.606 Water bridges: A:G.602 MPD.10: 4 residues within 4Å: Chain A: P.459, L.460, L.463, I.478 No protein-ligand interaction detected (PLIP)

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.11: 3 residues within 4Å: Chain A: T.3, Y.77, P.81 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.3

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

SO4.12: 5 residues within 4Å: Chain A: Q.346, K.347, E.403, R.406 Ligands: MPD.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.347 Water bridges: A:S.344 Salt bridges: A:R.406

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

CL.13: 4 residues within 4Å: Chain A: R.95, R.122, T.137, R.143 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: V.286 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: G.291, T.323 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: R.94, R.95 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tauchert, M.J. et al., Structural insights into the mechanism of the DEAH-box RNA helicase Prp43. Elife (2017)

Release Date

2017-01-25

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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