SMTL ID : 2c38.2 (3 other biounits)

RNase PH core of the archaeal exosome in complex with A5 RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-3-3-mer

Ligands

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

CL.1: 5 residues within 4Å: Chain B: R.99, G.137, S.138, R.139 Ligands: AMP.5 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain D: R.99, G.137, S.138, R.139 Ligands: AMP.10 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain F: R.99, G.137, S.138, R.139 Ligand excluded by PLIP

8 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 7 residues within 4Å: Chain A: Y.75, L.84, I.85, D.115, R.119 Chain B: R.98 Ligands: AMP.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.75, A:D.115, B:R.98 pi-Stacking: A:Y.75 AMP.3: 6 residues within 4Å: Chain A: R.112, D.115, R.119 Chain B: R.98 Ligands: AMP.2, AMP.4 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.98, A:R.112 Hydrogen bonds: A:R.112 AMP.4: 6 residues within 4Å: Chain A: R.112, R.116 Chain B: D.182, M.183 Ligands: AMP.3, AMP.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.99, B:D.182, B:D.182 Salt bridges: A:R.112 AMP.5: 13 residues within 4Å: Chain B: M.83, T.88, R.99, A.134, D.135, A.136, S.138, R.139, E.179, D.182, D.188 Ligands: CL.1, AMP.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.134, B:A.136, B:S.138 Salt bridges: B:R.99, B:R.139 AMP.7: 5 residues within 4Å: Chain C: Y.75, L.84, I.85 Chain D: R.98 Ligands: AMP.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D pi-Stacking: C:Y.75, C:Y.75 Hydrogen bonds: D:R.98 AMP.8: 6 residues within 4Å: Chain C: R.112, D.115, R.119 Chain D: R.98 Ligands: AMP.7, AMP.9 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.112 Salt bridges: C:R.112, D:R.98 AMP.9: 6 residues within 4Å: Chain C: R.112 Chain D: R.99, D.182, M.183 Ligands: AMP.8, AMP.10 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.112 AMP.10: 14 residues within 4Å: Chain D: M.83, T.88, K.92, R.99, A.134, D.135, A.136, S.138, R.139, E.179, D.182, D.188 Ligands: CL.6, AMP.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.88, D:A.134, D:A.136, D:S.138 Salt bridges: D:R.99, D:R.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorentzen, E. et al., Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core. Mol.Cell (2005)

Release Date

2005-11-23

Peptides

PROBABLE EXOSOME COMPLEX EXONUCLEASE 2: ACE
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
I

E
K

B
H

D
J

F
L

PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

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