SMTL ID : 5elx.1

S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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: 23 residues within 4Å: Chain A: P.80, S.81, R.82, P.108, T.125, P.126, G.127, T.128, D.131, Q.157, Q.158, G.159, L.160, Q.163, A.248, T.249, K.250, H.271, G.272, R.279, T.297, N.298, V.299 Protein-ligand interaction information (PLIP) not available

1 x M2A: [(2~{R},3~{R},4~{R},5~{S})-2-(6-aminopurin-9-yl)-4-oxidanyl-5-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] 2-(methylamino)benzoate(Non-covalent)

M2A.2: 20 residues within 4Å: Chain A: F.4, M.20, F.22, K.24, P.25, S.26, Q.29, Q.49, S.50, G.51, T.52, G.53, K.54, T.55, E.94, D.305, R.339, F.340 Ligands: MG.3, BEF.4 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:F.22 Hydrogen bonds: A:S.26, A:Q.29, A:Q.29, A:Q.49, A:G.51, A:T.52, A:G.53, A:K.54, A:T.55, A:T.55, A:T.55, A:D.305 Water bridges: A:Q.23, A:Q.23, A:A.56, A:Q.87, A:D.305, A:R.339, A:R.339, A:R.342, A:R.342 Salt bridges: A:K.54, A:R.339, A:R.339 pi-Stacking: A:F.22, A:F.22, A:F.340, A:F.340

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.55, D.149, E.150 Ligands: M2A.2, BEF.4 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: D.174 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.174, H2O.4, H2O.8, H2O.10

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

BEF.4: 10 residues within 4Å: Chain A: S.50, G.51, K.54, E.150, A.182, G.303, R.336, R.339 Ligands: M2A.2, MG.3 No protein-ligand interaction detected (PLIP)

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

NO3.5: 2 residues within 4Å: Chain A: R.42, N.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.42 NO3.6: 4 residues within 4Å: Chain A: I.165, K.168, R.169, I.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.168, A:R.169 Water bridges: A:K.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, E.V. et al., Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5). J.Mol.Biol. (2016)

Release Date

2016-02-24

Peptides

ATP-dependent RNA helicase DBP5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent RNA helicase DBP5