SMTL ID : 2jeb.1

Structure of a 9-subunit archaeal exosome bound to Mn ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-3-3-3-mer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 2 residues within 4Å: Chain A: E.72, D.74 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.74 MN.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.5: 2 residues within 4Å: Chain D: E.72, D.74 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.74 MN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.9: 2 residues within 4Å: Chain G: E.72, D.74 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.74 MN.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 6 residues within 4Å: Chain A: S.43, T.45, Y.48, L.57, K.59 Chain E: E.36 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.59, E:V.39 Water bridges: A:T.45 1PE.6: 6 residues within 4Å: Chain D: S.43, T.45, Y.48, L.57, K.59 Chain H: E.36 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:T.45, D:K.59, H:V.39 1PE.10: 6 residues within 4Å: Chain B: E.36 Chain G: S.43, T.45, Y.48, L.57, K.59 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:V.39, G:K.59 Water bridges: G:T.45

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

CL.3: 4 residues within 4Å: Chain B: R.101, G.139, S.140, R.141 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain E: R.101, G.139, S.140, R.141 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain H: R.101, G.139, S.140, R.141 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorentzen, E. et al., RNA Channelling by the Archaeal Exosome. Embo Rep. (2007)

Release Date

2007-04-03

Peptides

EXOSOME COMPLEX EXONUCLEASE 2: ADG
EXOSOME COMPLEX EXONUCLEASE 1: BEH
EXOSOME COMPLEX RNA-BINDING PROTEIN 1: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
I

F
I

I
I

EXOSOME COMPLEX EXONUCLEASE 2

EXOSOME COMPLEX EXONUCLEASE 1

EXOSOME COMPLEX RNA-BINDING PROTEIN 1

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