SMTL ID : 3pey.1

S. cerevisiae Dbp5 bound to RNA and ADP BeF3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x U- U- U- U- U- U: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')(Non-covalent)

U-U-U-U-U-U.1: 26 residues within 4Å: Chain A: P.83, S.84, R.85, P.111, T.128, P.129, G.130, T.131, D.134, Q.160, Q.161, G.162, L.163, Q.166, A.251, T.252, K.253, H.274, G.275, R.282, T.300, N.301, V.302, T.322, A.324 Ligands: NO3.11 Protein-ligand interaction information (PLIP) not available

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

ADP.2: 18 residues within 4Å: Chain A: F.7, F.25, K.27, P.28, S.29, Q.32, Q.52, S.53, G.54, T.55, G.56, K.57, T.58, D.308, R.342, F.343 Ligands: MG.3, BEF.4 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:K.27, A:S.29, A:Q.32, A:Q.52, A:G.54, A:T.55, A:G.56, A:K.57, A:T.58, A:T.58, A:T.58, A:D.308 Water bridges: A:Q.26, A:Q.26, A:A.59, A:Q.90, A:Q.90, A:R.342, A:R.345, A:R.345, A:R.345 Salt bridges: A:K.57, A:R.342, A:R.342 pi-Stacking: A:F.25, A:F.25, A:F.343, A:F.343

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.58, D.152, E.153 Ligands: ADP.2, BEF.4 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: D.177 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.177, H2O.5, H2O.5, H2O.6, H2O.9, H2O.9 MG.6: 1 residues within 4Å: Chain A: D.8 No protein-ligand interaction detected (PLIP)

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

BEF.4: 10 residues within 4Å: Chain A: S.53, G.54, K.57, E.153, A.185, G.306, R.339, R.342 Ligands: ADP.2, MG.3 No protein-ligand interaction detected (PLIP)

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 4 residues within 4Å: Chain A: I.168, K.171, R.172, I.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.171, A:R.172, A:R.172 Water bridges: A:K.171, A:K.171 NO3.8: 2 residues within 4Å: Chain A: R.45, N.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.45 NO3.9: 3 residues within 4Å: Chain A: R.137, R.169, F.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.137 Water bridges: A:R.169 NO3.11: 3 residues within 4Å: Chain A: Q.166 Ligands: U-U-U-U-U-U.1, U-U-U-U-U-U.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.166

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: Q.119, R.138, K.139, L.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Montpetit, B. et al., A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP(6) in mRNA export. Nature (2011)

Release Date

2011-03-23

Peptides

ATP-dependent RNA helicase DBP5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent RNA helicase DBP5