SMTL ID : 4ba2.1

Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x A- A- A- A: 5'-R(*AP*AP*AP*AP)-3'(Non-covalent)

A-A-A-A.1: 15 residues within 4Å: Chain A: Y.77, D.79, L.86, I.87, R.114, D.117, R.121 Chain B: T.90, R.100, R.101, A.136, A.138, R.141, E.181 Ligands: PO4.3 Protein-ligand interaction information (PLIP) not available A-A-A-A.6: 15 residues within 4Å: Chain D: Y.77, D.79, L.86, I.87, R.114, D.117, R.121 Chain E: T.90, R.100, R.101, A.136, A.138, R.141, E.181 Ligands: PO4.8 Protein-ligand interaction information (PLIP) not available A-A-A-A.11: 15 residues within 4Å: Chain G: Y.77, D.79, L.86, I.87, R.114, D.117, R.121 Chain H: T.90, R.100, R.101, A.136, A.138, R.141, E.181 Ligands: PO4.13 Protein-ligand interaction information (PLIP) not available

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

1PE.2: 8 residues within 4Å: Chain A: S.43, T.45, Y.48, L.57, K.59, M.64 Chain H: E.36, V.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.45, A:K.59 1PE.7: 8 residues within 4Å: Chain B: E.36, V.39 Chain D: S.43, T.45, Y.48, L.57, K.59, M.64 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.59 Water bridges: D:T.45 1PE.12: 8 residues within 4Å: Chain E: E.36, V.39 Chain G: S.43, T.45, Y.48, L.57, K.59, M.64 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:K.59 Water bridges: G:T.45

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain B: R.101, A.138, G.139, S.140, R.141 Ligands: A-A-A-A.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.139, B:S.140, B:R.141 Salt bridges: B:R.101, B:R.141 PO4.5: 2 residues within 4Å: Chain C: D.57, T.58 No protein-ligand interaction detected (PLIP) PO4.8: 6 residues within 4Å: Chain E: R.101, A.138, G.139, S.140, R.141 Ligands: A-A-A-A.6 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.139, E:S.140, E:R.141 Salt bridges: E:R.101, E:R.141 PO4.10: 2 residues within 4Å: Chain F: D.57, T.58 No protein-ligand interaction detected (PLIP) PO4.13: 6 residues within 4Å: Chain H: R.101, A.138, G.139, S.140, R.141 Ligands: A-A-A-A.11 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:G.139, H:S.140, H:R.141 Salt bridges: H:R.101, H:R.141 PO4.15: 2 residues within 4Å: Chain I: D.57, T.58 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.58

3 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: S.4, E.107 Chain B: I.103, S.106, K.107 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.107, A:E.107, A:E.107 NA.9: 5 residues within 4Å: Chain D: S.4, E.107 Chain E: I.103, S.106, K.107 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.103, E:K.107 NA.14: 5 residues within 4Å: Chain G: S.4, E.107 Chain H: I.103, S.106, K.107 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:E.107, G:E.107, H:K.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorentzen, E. et al., Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction. Archaea (2012)

Release Date

2012-10-03

Peptides

PROBABLE EXOSOME COMPLEX EXONUCLEASE 2: ADG
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1: BEH
PROBABLE 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

PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1

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