SMTL ID : 4w7s.1

Crystal structure of the yeast DEAD-box splicing factor Prp28 at 2.54 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

homo-dimer

Ligands

8 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.1: 7 residues within 4Å: Chain A: V.36, K.38, M.256, E.261, Y.273, A.274, T.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.38, A:T.275 Water bridges: A:K.38 P6G.2: 4 residues within 4Å: Chain A: I.126, H.203, L.204, V.206 No protein-ligand interaction detected (PLIP) P6G.3: 5 residues within 4Å: Chain A: Q.287, V.289, I.306, K.309, Y.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.287, A:Q.287 P6G.4: 7 residues within 4Å: Chain A: W.13, T.14, Y.33, R.47, N.48, S.71, R.77 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.48 Hydrogen bonds: A:N.48, A:S.71, A:R.77 P6G.5: 8 residues within 4Å: Chain A: D.228, Q.229, N.232 Chain B: I.222, D.223, L.224, G.225, V.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.229, A:N.232 P6G.8: 6 residues within 4Å: Chain B: V.36, K.38, M.256, E.261, Y.273, T.275 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.38 P6G.9: 3 residues within 4Å: Chain B: E.23, R.24, R.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.27 Water bridges: B:E.23, B:R.27 P6G.10: 5 residues within 4Å: Chain B: T.14, K.16, R.47, N.48, E.51 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.48 Water bridges: B:Y.33, B:S.71

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: S.183, E.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.184

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.7: 13 residues within 4Å: Chain B: W.49, F.69, S.71, P.72, T.73, Q.76, G.99, S.100, G.101, Q.144, E.148, K.151 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.71, B:T.73, B:Q.76, B:S.100, B:G.101, B:Q.144, B:E.148, B:E.148, B:K.151 Water bridges: B:T.103, B:T.103 pi-Stacking: B:F.69, B:F.69

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.11: 1 residues within 4Å: Ligands: ANP.7 No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacewicz, A. et al., Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28. Nucleic Acids Res. (2014)

Release Date

2014-10-29

Peptides

Pre-mRNA-splicing ATP-dependent RNA helicase PRP28: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pre-mRNA-splicing ATP-dependent RNA helicase PRP28