SMTL ID : 4d26.1

Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA,ADP and Pi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x U- G- A- C- A- U: 5'-R(*UP*GP*AP*CP*AP*UP)-3'(Non-covalent)

U-G-A-C-A-U.1: 22 residues within 4Å: Chain A: V.5, P.135, T.136, R.137, G.163, G.164, V.167, T.184, P.185, G.186, R.187, D.190, F.218, E.309, T.310, K.311, H.332, G.333, R.340, T.358, A.359, V.360 Protein-ligand interaction information (PLIP) not available

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

ADP.2: 21 residues within 4Å: Chain A: T.23, I.24, F.30, F.52, Y.70, K.72, P.73, T.74, Q.77, Q.95, T.96, G.97, S.98, G.99, K.100, T.101, D.366, R.394, V.395 Ligands: PO4.3, MG.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:I.24, A:Y.70, A:T.74, A:Q.77, A:Q.77, A:Q.95, A:G.97, A:S.98, A:G.99, A:K.100, A:T.101, A:T.101, A:T.101, A:D.366 Water bridges: A:A.102, A:D.208, A:R.394, A:R.394 Salt bridges: A:K.100, A:R.394, A:R.394 pi-Stacking: A:Y.70, A:Y.70

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 11 residues within 4Å: Chain A: T.96, G.97, K.100, Q.209, A.244, G.364, H.387, R.391, R.394 Ligands: ADP.2, MG.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.97, A:Q.209, A:G.364 Water bridges: A:K.100, A:A.244, A:G.364, A:R.394 Salt bridges: A:K.100, A:H.387, A:R.391, A:R.394

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: K.100, D.208, Q.209 Ligands: ADP.2, PO4.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiol, J. et al., RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts. Cell(Cambridge,Mass.) (2014)

Release Date

2014-06-18

Peptides

BMVLG PROTEIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BMVLG PROTEIN

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