SMTL ID : 3llm.1

Crystal Structure Analysis of a RNA Helicase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: T.90, D.183, E.184 Ligands: ADP.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.90, A:E.184, H2O.11, H2O.12, H2O.13 MN.4: 4 residues within 4Å: Chain B: T.90, D.183, E.184 Ligands: ADP.5 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.90, B:E.184, H2O.22, H2O.23, H2O.25

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.2: 2 residues within 4Å: Chain A: D.47, D.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.47

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

ADP.3: 10 residues within 4Å: Chain A: L.60, T.85, G.86, C.87, G.88, K.89, T.90, T.91, R.128 Ligands: MN.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.84, A:G.86, A:G.86, A:C.87, A:G.88, A:G.88, A:K.89, A:T.90, A:T.91, A:T.91 Water bridges: A:K.89, A:K.89, A:S.124, A:S.124 Salt bridges: A:K.89 pi-Cation interactions: A:R.128 ADP.5: 11 residues within 4Å: Chain B: L.60, A.84, T.85, G.86, C.87, G.88, K.89, T.90, T.91, R.128 Ligands: MN.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.86, B:G.86, B:C.87, B:G.88, B:K.89, B:T.90, B:T.90, B:T.91, B:R.128 Water bridges: B:K.89, B:T.90 Salt bridges: B:K.89 pi-Cation interactions: B:R.128, B:R.128

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain B: Q.75, N.76, S.77, P.207, R.210 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.77, B:S.77, B:R.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schutz, P. et al., Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein. J.Mol.Biol. (2010)

Release Date

2010-05-12

Peptides

ATP-dependent RNA helicase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent RNA helicase A