SMTL ID : 2pnz.1

Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-3-3-mer

Ligands

3 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 12 residues within 4Å: Chain A: M.81, V.86, R.97, A.132, D.133, A.134, G.135, T.136, R.137, K.177, D.180, D.186 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.134, A:G.135, A:T.136, A:T.136, A:R.137, A:D.186 Water bridges: A:E.87, A:E.88, A:R.97, A:R.137, A:K.177, A:D.180, A:D.204 Salt bridges: A:R.97, A:R.97, A:R.137, A:R.137 UDP.8: 12 residues within 4Å: Chain C: M.81, V.86, R.97, A.132, D.133, A.134, G.135, T.136, R.137, K.177, D.180, D.186 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:A.134, C:G.135, C:T.136, C:T.136, C:R.137, C:D.186 Water bridges: C:E.87, C:E.88, C:R.97, C:R.137, C:K.177, C:D.180, C:D.204 Salt bridges: C:R.97, C:R.97, C:R.137, C:R.137 UDP.15: 12 residues within 4Å: Chain E: M.81, V.86, R.97, A.132, D.133, A.134, G.135, T.136, R.137, K.177, D.180, D.186 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:A.134, E:G.135, E:T.136, E:T.136, E:R.137, E:D.186 Water bridges: E:E.87, E:E.88, E:R.97, E:R.137, E:K.177, E:D.180, E:D.204 Salt bridges: E:R.97, E:R.97, E:R.137, E:R.137

3 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.2: 7 residues within 4Å: Chain A: R.89, K.91 Chain B: E.72, P.73, F.74, T.84, F.140 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Water bridges: A:R.89, A:R.89, A:R.89, A:R.89 Salt bridges: A:R.89, A:K.91 Hydrogen bonds: B:E.72, B:E.72 pi-Cation interactions: B:F.74 5GP.9: 7 residues within 4Å: Chain C: R.89, K.91 Chain D: E.72, P.73, F.74, T.84, F.140 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:E.72, D:E.72 pi-Cation interactions: D:F.74 Water bridges: C:R.89, C:R.89, C:R.89, C:R.89 Salt bridges: C:R.89, C:K.91 5GP.16: 7 residues within 4Å: Chain E: R.89, K.91 Chain F: E.72, P.73, F.74, T.84, F.140 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain F Water bridges: E:R.89, E:R.89, E:R.89, E:R.89 Salt bridges: E:R.89, E:K.91 Hydrogen bonds: F:E.72, F:E.72 pi-Cation interactions: F:F.74

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

MPD.3: 8 residues within 4Å: Chain A: D.180, N.181, G.183, E.184, A.185, D.204, G.205 Chain D: E.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.180, A:G.183 Water bridges: A:G.183 MPD.4: 5 residues within 4Å: Chain A: Y.24, L.173, K.221, G.222, A.225 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.173, A:K.221, A:K.221, A:A.225 Water bridges: A:L.26 MPD.5: 6 residues within 4Å: Chain A: R.76, V.77, R.78, D.124, F.126 Chain B: P.99 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.76, A:R.78, A:F.126, A:F.126 MPD.6: 6 residues within 4Å: Chain B: L.165, V.192, E.193, K.194, I.195, E.230 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.165, B:I.195 Hydrogen bonds: B:E.230, B:E.230 MPD.7: 4 residues within 4Å: Chain B: F.33, N.206, L.208, Y.252 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.33, B:L.208 Hydrogen bonds: B:L.208 MPD.10: 8 residues within 4Å: Chain C: D.180, N.181, G.183, E.184, A.185, D.204, G.205 Chain F: E.119 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.180, C:G.183 Water bridges: C:G.183 MPD.11: 5 residues within 4Å: Chain C: Y.24, L.173, K.221, G.222, A.225 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.173, C:K.221, C:K.221, C:A.225 Water bridges: C:L.26 MPD.12: 6 residues within 4Å: Chain C: R.76, V.77, R.78, D.124, F.126 Chain D: P.99 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.76, C:R.78, C:F.126, C:F.126 MPD.13: 6 residues within 4Å: Chain D: L.165, V.192, E.193, K.194, I.195, E.230 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.165, D:I.195 Hydrogen bonds: D:E.230, D:E.230 MPD.14: 4 residues within 4Å: Chain D: F.33, N.206, L.208, Y.252 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.33, D:L.208 Hydrogen bonds: D:L.208 MPD.17: 8 residues within 4Å: Chain B: E.119 Chain E: D.180, N.181, G.183, E.184, A.185, D.204, G.205 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.180, E:G.183 Water bridges: E:G.183 MPD.18: 5 residues within 4Å: Chain E: Y.24, L.173, K.221, G.222, A.225 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.173, E:K.221, E:K.221, E:A.225 Water bridges: E:L.26 MPD.19: 6 residues within 4Å: Chain E: R.76, V.77, R.78, D.124, F.126 Chain F: P.99 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:R.76, E:R.78, E:F.126, E:F.126 MPD.20: 6 residues within 4Å: Chain F: L.165, V.192, E.193, K.194, I.195, E.230 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.165, F:I.195 Hydrogen bonds: F:E.230, F:E.230 MPD.21: 4 residues within 4Å: Chain F: F.33, N.206, L.208, Y.252 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.33, F:L.208 Hydrogen bonds: F:L.208

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: ACE
Probable exosome complex exonuclease 2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Probable exosome complex exonuclease 1

Probable exosome complex exonuclease 2

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