SMTL ID : 1udn.1

Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: G.124, T.125, R.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.124, A:T.125, A:T.125, A:R.126 Salt bridges: A:R.126 PO4.4: 3 residues within 4Å: Chain B: G.124, T.125, R.126 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.124, B:T.125, B:T.125, B:R.126 Salt bridges: B:R.126 PO4.7: 3 residues within 4Å: Chain C: G.124, T.125, R.126 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.124, C:T.125, C:T.125, C:R.126 Salt bridges: C:R.126 PO4.10: 3 residues within 4Å: Chain D: G.124, T.125, R.126 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.124, D:T.125, D:T.125, D:R.126 Salt bridges: D:R.126 PO4.13: 3 residues within 4Å: Chain E: G.124, T.125, R.126 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.124, E:T.125, E:T.125, E:R.126 Salt bridges: E:R.126 PO4.16: 3 residues within 4Å: Chain F: G.124, T.125, R.126 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.124, F:T.125, F:T.125, F:R.126 Salt bridges: F:R.126

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: V.102, E.103, L.104, T.105, K.156 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:L.104, A:T.105, A:T.105 Salt bridges: A:K.156 Water bridges: E:E.206, E:E.206 SO4.3: 4 residues within 4Å: Chain A: W.58, T.60, R.92, R.99 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.60 Water bridges: A:W.58, A:A.61, A:A.61 Salt bridges: A:R.99 SO4.5: 5 residues within 4Å: Chain B: V.102, E.103, L.104, T.105, K.156 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B Water bridges: D:E.206, D:E.206 Hydrogen bonds: B:L.104, B:T.105, B:T.105 Salt bridges: B:K.156 SO4.6: 4 residues within 4Å: Chain B: W.58, T.60, R.92, R.99 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.60 Water bridges: B:W.58, B:A.61, B:A.61 Salt bridges: B:R.99 SO4.8: 5 residues within 4Å: Chain C: V.102, E.103, L.104, T.105, K.156 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:L.104, C:T.105, C:T.105 Salt bridges: C:K.156 Water bridges: F:E.206, F:E.206 SO4.9: 4 residues within 4Å: Chain C: W.58, T.60, R.92, R.99 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.60 Water bridges: C:W.58, C:A.61, C:A.61 Salt bridges: C:R.99 SO4.11: 5 residues within 4Å: Chain D: V.102, E.103, L.104, T.105, K.156 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.104, D:T.105 Salt bridges: D:K.156 SO4.12: 4 residues within 4Å: Chain D: W.58, T.60, R.92, R.99 5 PLIP interactions: 5 interactions with chain D Water bridges: D:W.58, D:T.60, D:A.61, D:A.61 Salt bridges: D:R.99 SO4.14: 5 residues within 4Å: Chain E: V.102, E.103, L.104, T.105, K.156 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.104, E:T.105 Salt bridges: E:K.156 SO4.15: 4 residues within 4Å: Chain E: W.58, T.60, R.92, R.99 5 PLIP interactions: 5 interactions with chain E Water bridges: E:W.58, E:T.60, E:A.61, E:A.61 Salt bridges: E:R.99 SO4.17: 5 residues within 4Å: Chain F: V.102, E.103, L.104, T.105, K.156 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:L.104, F:T.105 Salt bridges: F:K.156 SO4.18: 4 residues within 4Å: Chain F: W.58, T.60, R.92, R.99 5 PLIP interactions: 5 interactions with chain F Water bridges: F:W.58, F:T.60, F:A.61, F:A.61 Salt bridges: F:R.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishii, R. et al., Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus. J.Biol.Chem. (2003)

Release Date

2003-09-23

Peptides

Ribonuclease PH: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Ribonuclease PH