SMTL ID : 3ex7.2 (1 other biounit)

The crystal structure of EJC in its transition state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x U- U- U- U- U- U: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')(Non-covalent)

U-U-U-U-U-U.1: 28 residues within 4Å: Chain C: P.114, T.115, R.116, I.141, G.142, G.143, T.144, V.146, T.163, P.164, G.165, R.166, D.169, R.172, F.197, Q.200, N.285, T.286, K.287, H.308, G.309, R.316, T.334, D.335, V.336, N.356 Chain D: P.46, F.51 Protein-ligand interaction information (PLIP) not available

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

ADP.2: 19 residues within 4Å: Chain C: F.40, Y.56, F.58, K.60, P.61, S.62, Q.65, Q.83, G.85, T.86, G.87, K.88, T.89, A.90, D.342, R.370, Y.371 Ligands: AF3.3, MG.4 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:K.60, C:S.62, C:Q.65, C:S.82, C:S.82, C:G.85, C:T.86, C:G.87, C:K.88, C:T.89, C:A.90, C:D.342, C:D.342 Water bridges: C:E.59, C:K.88, C:K.88, C:T.89, C:T.89 Salt bridges: C:K.88, C:R.370, C:R.370 pi-Stacking: C:F.58, C:F.58, C:Y.371, C:Y.371

1 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 10 residues within 4Å: Chain C: S.84, G.85, K.88, E.188, A.219, G.340, R.367, R.370 Ligands: ADP.2, MG.4 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain C: T.89, D.187 Ligands: ADP.2, AF3.3 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.89, H2O.4, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nielsen, K.H. et al., Mechanism of ATP turnover inhibition in the EJC. Rna (2009)

Release Date

2008-12-09

Peptides

Protein mago nashi homolog: A
RNA-binding protein 8A: B
Eukaryotic initiation factor 4A-III: C
Protein CASC3: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
G

C
H

D
I

Protein mago nashi homolog

RNA-binding protein 8A

Eukaryotic initiation factor 4A-III

Protein CASC3

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