SMTL ID : 2xzo.1

Upf1 helicase - RNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

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

U-U-U-U-U-U-U.1: 28 residues within 4Å: Chain A: Y.25, L.29, K.30, K.125, T.127, S.128, R.131, P.231, S.232, N.233, A.255, K.256, S.257, R.258, T.325, V.327, V.378, M.380, T.471, S.472, P.504, Y.505, E.506, S.534, D.536, A.537, G.560, F.561 Protein-ligand interaction information (PLIP) not available

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 9 residues within 4Å: Chain A: N.181, H.182, S.183, Q.184, T.205, L.407, Q.408, V.409, Y.411 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.181, A:H.182, A:S.183, A:S.183, A:T.205, A:Q.408, A:V.409 1PE.3: 4 residues within 4Å: Chain A: R.171, T.173, A.174, Q.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.171 1PE.4: 6 residues within 4Å: Chain A: D.130, R.131, S.134, A.135, G.330, V.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.131, A:S.134

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

ADP.5: 17 residues within 4Å: Chain A: P.178, D.179, L.180, N.181, Q.184, P.202, G.204, T.205, G.206, K.207, T.208, V.209, Y.411, R.412, E.542 Ligands: ALF.6, MG.7 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.181, A:Q.184, A:Q.184, A:G.204, A:T.205, A:G.206, A:K.207, A:T.208, A:V.209, A:E.542 Water bridges: A:K.242, A:R.412, A:R.412, A:G.540 Salt bridges: A:K.207, A:K.242, A:R.412, A:R.412 pi-Stacking: A:Y.411

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.6: 10 residues within 4Å: Chain A: P.203, G.204, K.207, E.346, Q.374, R.412, G.540, R.574 Ligands: ADP.5, MG.7 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: T.208 Ligands: ADP.5, ALF.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.208, H2O.1, H2O.1, H2O.4 MG.8: 8 residues within 4Å: Chain A: Y.515, M.516, Q.517, F.518, S.519, G.520, S.521, T.524 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:M.516

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chakrabarti, S. et al., Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2. Mol.Cell (2011)

Release Date

2011-03-30

Peptides

REGULATOR OF NONSENSE TRANSCRIPTS 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

REGULATOR OF NONSENSE TRANSCRIPTS 1

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