SMTL ID : 8enk.1

Crystal structure of UAP56 in complex with Tho1, the yeast homolog of human SARNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-1-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: F.9, F.27, H.29, Q.34, K.52, S.53, G.54, M.55, G.56, K.57, T.58, R.97, D.314, R.342, F.343 Ligands: BEF.2, MG.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Q.34, A:Q.34, A:G.54, A:M.55, A:G.56, A:K.57, A:T.58, A:T.58, A:T.58, A:R.97, A:R.97, A:D.314 Water bridges: A:D.158, A:R.342, A:R.342 Salt bridges: A:K.57, A:R.342, A:R.342 pi-Stacking: A:F.27, A:F.27, A:F.343, A:F.343 ADP.4: 16 residues within 4Å: Chain B: F.9, F.27, H.29, P.30, Q.34, G.54, M.55, G.56, K.57, T.58, R.97, D.314, R.342, F.343 Ligands: BEF.5, MG.6 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:H.29, B:Q.34, B:G.54, B:M.55, B:G.56, B:K.57, B:T.58, B:T.58, B:T.58, B:R.97, B:D.314 Water bridges: B:A.59, B:R.342, B:R.342 Salt bridges: B:K.57, B:R.342, B:R.342 pi-Stacking: B:F.27, B:F.27, B:F.343

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 9 residues within 4Å: Chain A: G.54, K.57, E.159, A.191, G.312, R.339, R.342 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 10 residues within 4Å: Chain B: S.53, G.54, K.57, E.159, A.191, G.312, R.339, R.342 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.58, D.158, E.159 Ligands: ADP.1, BEF.2 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain B: T.58, D.158, E.159, G.312 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, Y. et al., Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly. Cell Rep (2023)

Release Date

2023-08-16

Peptides

Spliceosome RNA helicase DDX39B: AB
Protein THO1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Spliceosome RNA helicase DDX39B

Protein THO1