SMTL ID : 6l5n.2 (1 other biounit)

Crystal structure of human DEAD-box RNA helicase DDX21 at post-unwound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

monomer

Ligands

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

ANP.1: 22 residues within 4Å: Chain A: R.18, G.19, V.20, F.22, F.24, Q.27, R.45, T.46, G.47, T.48, G.49, K.50, T.51, F.52, E.154, A.190, G.314, D.316, R.341, R.344, A.345 Ligands: MG.3 35 PLIP interactions: 35 interactions with chain A Hydrogen bonds: A:R.18, A:F.22, A:F.24, A:Q.27, A:G.47, A:T.48, A:T.48, A:G.49, A:K.50, A:K.50, A:K.50, A:T.51, A:T.51, A:G.314, A:G.314, A:D.316, A:R.341, A:R.341, A:R.344, A:R.344 Water bridges: A:T.21, A:K.50, A:F.52, A:Q.89, A:Q.89, A:Q.89, A:Q.89, A:D.93, A:E.154, A:A.190, A:H.337, A:R.347 Salt bridges: A:R.344 pi-Stacking: A:F.24, A:F.24 ANP.2: 6 residues within 4Å: Chain A: D.160, M.161, H.194, W.195, K.369 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.160, A:D.160, A:K.369, A:K.369 Water bridges: A:K.330, A:D.331, A:D.331, A:V.332, A:K.369 pi-Stacking: A:W.195, A:W.195, A:W.195

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.51, D.153, E.154 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: D.331 Ligands: ANP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. Adv Sci (2020)

Release Date

2020-06-17

Peptides

Nucleolar RNA helicase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nucleolar RNA helicase 2

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