SMTL ID : 4oo1.1

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain E: D.85, I.86, Q.89, D.91 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.85, E:Q.89 MG.5: 3 residues within 4Å: Chain J: N.113 Chain K: A.5, A.6 No protein-ligand interaction detected (PLIP)

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

MPD.2: 4 residues within 4Å: Chain E: K.12, S.13, Y.16, N.239 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.239

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 7 residues within 4Å: Chain A: K.13 Chain G: D.156, G.157, C.202, E.203, L.205, T.208 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain G Salt bridges: A:K.13 Hydrogen bonds: G:G.157

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

PO4.4: 2 residues within 4Å: Chain I: R.154 Ligands: PO4.6 No protein-ligand interaction detected (PLIP) PO4.6: 2 residues within 4Å: Chain K: A.1 Ligands: PO4.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wasmuth, E.V. et al., Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA. Nature (2014)

Release Date

2014-07-02

Peptides

Exosome complex component RRP45: A
Exosome complex component SKI6: B
Exosome complex component RRP43: C
Exosome complex component RRP46: D
Exosome complex component RRP42: E
Exosome complex component MTR3: F
Exosome complex component RRP40: G
Exosome complex component RRP4: H
Exosome complex component CSL4: I
Exosome complex exonuclease RRP6: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Exosome complex component RRP45

Exosome complex component SKI6

Exosome complex component RRP43

Exosome complex component RRP46

Exosome complex component RRP42

Exosome complex component MTR3

Exosome complex component RRP40

Exosome complex component RRP4

Exosome complex component CSL4

Exosome complex exonuclease RRP6

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