SMTL ID : 4d25.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 25 residues within 4Å: Chain A: P.135, T.136, R.137, Y.162, G.163, G.164, V.167, T.184, P.185, G.186, R.187, D.190, R.194, G.217, F.218, E.309, T.310, K.311, H.332, G.333, R.340, T.358, A.359, V.360 Ligands: GOL.4 Protein-ligand interaction information (PLIP) not available

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

ANP.2: 23 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, Q.209, G.364, D.366, R.391, R.394, V.395 Ligands: MG.3 37 PLIP interactions: 37 interactions with chain A Hydrogen bonds: A:T.23, A:I.24, A:T.74, A:Q.77, A:Q.77, A:G.97, A:S.98, A:G.99, A:K.100, A:K.100, A:T.101, A:T.101, A:T.101, A:K.149, A:Q.209, A:G.364, A:D.366, A:R.391, A:R.391, A:R.394, A:R.394 Water bridges: A:Y.70, A:R.71, A:R.71, A:A.102, A:Q.142, A:Q.142, A:Q.142, A:Q.142, A:E.146, A:Q.209, A:H.387, A:H.387, A:H.387 Salt bridges: A:R.394 pi-Stacking: A:Y.70, A:Y.70

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.101, D.208, Q.209 Ligands: ANP.2 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: C.212, A.359, R.363 Ligands: U-G-A-C-A-U.1, U-G-A-C-A-U.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.363 Water bridges: A:R.363

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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