SMTL ID : 3dm5.2 (4 other biounits)

Structures of SRP54 and SRP19, the two proteins assembling the ribonucleic core of the Signal Recognition Particle from the archaeon Pyrococcus furiosus.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.126, R.127 Chain B: D.380 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.126, A:R.127 SO4.2: 2 residues within 4Å: Chain A: R.288, R.292 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.292 SO4.3: 1 residues within 4Å: Chain A: H.145 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.145 SO4.4: 1 residues within 4Å: Chain A: R.33 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.33 SO4.5: 2 residues within 4Å: Chain A: D.197, K.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.198 Salt bridges: A:K.198 SO4.6: 1 residues within 4Å: Chain A: K.205 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.205 SO4.9: 3 residues within 4Å: Chain A: D.380 Chain B: K.126, R.127 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.126, B:R.127 SO4.10: 2 residues within 4Å: Chain B: R.288, R.292 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.292 SO4.11: 1 residues within 4Å: Chain B: H.145 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.145 SO4.12: 1 residues within 4Å: Chain B: R.33 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.33 SO4.13: 2 residues within 4Å: Chain B: D.197, K.198 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.198 Salt bridges: B:K.198 SO4.14: 1 residues within 4Å: Chain B: K.205 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.205

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 2 residues within 4Å: Chain A: R.122, Q.125 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.122 ACT.15: 2 residues within 4Å: Chain B: R.122, Q.125 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.122

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.8: 16 residues within 4Å: Chain A: Q.109, G.110, S.111, G.112, K.113, T.114, T.115, K.119, R.140, Q.146, K.248, D.250, G.273, T.274, G.275, E.276 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.110, A:S.111, A:G.112, A:K.113, A:T.114, A:T.114, A:T.114, A:T.115, A:T.115, A:K.119, A:Q.146, A:K.248, A:K.248, A:G.275 Water bridges: A:I.108, A:K.113, A:R.140, A:R.140, A:E.276, A:E.276 Salt bridges: A:K.113, A:R.140, A:D.250, A:E.276 GDP.16: 16 residues within 4Å: Chain B: Q.109, G.110, S.111, G.112, K.113, T.114, T.115, K.119, R.140, Q.146, K.248, D.250, G.273, T.274, G.275, E.276 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.110, B:S.111, B:G.112, B:K.113, B:T.114, B:T.114, B:T.114, B:T.115, B:T.115, B:K.119, B:Q.146, B:K.248, B:K.248, B:G.275 Water bridges: B:I.108, B:K.113, B:R.140, B:R.140, B:E.276, B:E.276 Salt bridges: B:K.113, B:R.140, B:D.250, B:E.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egea, P.F. et al., Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus. Plos One (2008)

Release Date

2008-11-04

Peptides

Signal recognition 54 kDa protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Signal recognition 54 kDa protein

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