SMTL ID : 8ejm.1

Crystal structure of human DEAH-box helicase DHX15 in complex with SUGP1 G-patch

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: E.52, T.53, G.54, S.55, G.56, K.57, T.58, T.59, S.91, R.95, F.292, T.320, D.322 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.54, A:S.55, A:G.56, A:K.57, A:T.58, A:T.58, A:T.59, A:S.91, A:D.322 Water bridges: A:K.57, A:T.58, A:R.95, A:R.95, A:D.151, A:E.152, A:T.317 Salt bridges: A:K.57 pi-Stacking: A:F.292

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: V.42, R.43, H.44, Q.45, K.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.44, A:K.178, A:K.178 GOL.3: 5 residues within 4Å: Chain A: I.112, R.113, T.128, G.130, M.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.113 Water bridges: A:G.130

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: T.58, D.151, E.152, S.318 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.58, H2O.1, H2O.2, H2O.2, H2O.5

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: R.493, K.498 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.493, A:K.498 SO4.6: 4 residues within 4Å: Chain A: I.578, K.582, K.645, W.648 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.648 Salt bridges: A:K.582, A:K.645

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: R.17, R.95 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.343, Y.436, K.605 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-12-14

Peptides

ATP-dependent RNA helicase DHX15: A
SURP and G-patch domain-containing protein 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent RNA helicase DHX15

SURP and G-patch domain-containing protein 1