SMTL ID : 2po1.1

Crystal structure of the P. abyssi exosome RNase PH ring complexed with a single stranded 10-mer poly(A) RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-3-3-mer

Ligands

15 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 10 residues within 4Å: Chain A: A.8, A.9 Chain B: D.180, G.183, E.184, A.185, D.186, D.204, G.205 Chain I: E.119 Ligand excluded by PLIP MPD.2: 7 residues within 4Å: Chain B: V.35, Y.44, I.53 Chain C: L.54, K.56, Q.61, L.146 Ligand excluded by PLIP MPD.3: 7 residues within 4Å: Chain C: L.165, V.192, E.193, K.194, I.195, E.230, L.269 Ligand excluded by PLIP MPD.4: 5 residues within 4Å: Chain C: F.33, N.206, L.208, E.249, Y.252 Ligand excluded by PLIP MPD.5: 1 residues within 4Å: Chain C: K.259 Ligand excluded by PLIP MPD.6: 10 residues within 4Å: Chain C: E.119 Chain D: A.8, A.9 Chain E: D.180, G.183, E.184, A.185, D.186, D.204, G.205 Ligand excluded by PLIP MPD.7: 7 residues within 4Å: Chain E: V.35, Y.44, I.53 Chain F: L.54, K.56, Q.61, L.146 Ligand excluded by PLIP MPD.8: 7 residues within 4Å: Chain F: L.165, V.192, E.193, K.194, I.195, E.230, L.269 Ligand excluded by PLIP MPD.9: 5 residues within 4Å: Chain F: F.33, N.206, L.208, E.249, Y.252 Ligand excluded by PLIP MPD.10: 1 residues within 4Å: Chain F: K.259 Ligand excluded by PLIP MPD.11: 10 residues within 4Å: Chain F: E.119 Chain G: A.8, A.9 Chain H: D.180, G.183, E.184, A.185, D.186, D.204, G.205 Ligand excluded by PLIP MPD.12: 7 residues within 4Å: Chain H: V.35, Y.44, I.53 Chain I: L.54, K.56, Q.61, L.146 Ligand excluded by PLIP MPD.13: 7 residues within 4Å: Chain I: L.165, V.192, E.193, K.194, I.195, E.230, L.269 Ligand excluded by PLIP MPD.14: 5 residues within 4Å: Chain I: F.33, N.206, L.208, E.249, Y.252 Ligand excluded by PLIP MPD.15: 1 residues within 4Å: Chain I: K.259 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Navarro, M.V.A.S. et al., Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J.Biol.Chem. (2008)

Release Date

2008-03-18

Peptides

Probable exosome complex exonuclease 1: BEH
Probable exosome complex exonuclease 2: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

E
A

H
A

C
B

F
B

I
B

Probable exosome complex exonuclease 1

Probable exosome complex exonuclease 2

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