SMTL ID : 3dmd.1 (3 other biounits)

Structures and Conformations in Solution of the Signal Recognition Particle Receptor from the archaeon Pyrococcus furiosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: N.138, G.139, S.140, G.141, K.142, T.143, R.169 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: A.69, L.70, R.262 Chain E: R.227, K.235 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: F.168, R.169, A.170, R.222 Chain C: Y.192 Ligands: GOL.4 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain B: N.138, G.139, S.140, G.141, K.142, T.143, R.169 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain B: A.69, L.70, R.262 Chain C: R.227, K.235 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain B: F.168, R.169, A.170, R.222 Chain E: Y.192 Ligands: GOL.8 Ligand excluded by PLIP SO4.9: 8 residues within 4Å: Chain C: F.137, N.138, G.139, S.140, G.141, K.142, T.143, R.169 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain C: A.69, L.70, R.262 Chain D: K.235 Ligand excluded by PLIP SO4.11: 1 residues within 4Å: Chain C: R.90 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain C: N.138, R.222 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain D: F.137, N.138, G.139, S.140, G.141, K.142, T.143, R.169 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain D: D.40, R.41 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain D: N.138, R.222 Ligand excluded by PLIP SO4.21: 8 residues within 4Å: Chain E: F.137, N.138, G.139, S.140, G.141, K.142, T.143, R.169 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain E: A.69, L.70, R.262 Chain F: K.235 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain E: R.90 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain E: N.138, R.222 Ligand excluded by PLIP SO4.26: 8 residues within 4Å: Chain F: F.137, N.138, G.139, S.140, G.141, K.142, T.143, R.169 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain F: D.40, R.41 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain F: N.138, R.222 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: N.138, R.169, R.222 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.138, A:R.169, A:R.169, A:R.222 GOL.8: 4 residues within 4Å: Chain B: N.138, R.169, R.222 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.138, B:R.169, B:R.169, B:R.222 GOL.13: 7 residues within 4Å: Chain A: Y.192 Chain C: F.168, R.169, A.170, G.171, A.172, R.222 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain C Water bridges: A:Y.192, C:A.170 Hydrogen bonds: C:F.168, C:R.169, C:G.171, C:A.172, C:R.222, C:R.222 GOL.17: 6 residues within 4Å: Chain D: F.168, R.169, G.171, A.172, R.222 Chain F: Y.192 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:G.171, D:A.172, D:R.222, D:R.222, F:Y.192 Water bridges: D:Y.192 GOL.18: 3 residues within 4Å: Chain D: W.152, H.156, P.312 No protein-ligand interaction detected (PLIP) GOL.19: 6 residues within 4Å: Chain B: R.227, K.235 Chain D: A.69, L.70, E.71, R.262 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.70 Water bridges: D:G.254 GOL.20: 4 residues within 4Å: Chain C: E.65 Chain D: H.190, S.191, A.194 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.65, D:S.191 Water bridges: C:E.65, C:E.65 GOL.25: 7 residues within 4Å: Chain B: Y.192 Chain E: F.168, R.169, A.170, G.171, A.172, R.222 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:F.168, E:R.169, E:G.171, E:A.172, E:R.222, E:R.222, B:Y.192 Water bridges: E:A.170, E:Y.192 GOL.29: 6 residues within 4Å: Chain D: Y.192 Chain F: F.168, R.169, G.171, A.172, R.222 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.171, F:A.172, F:R.222, F:R.222 GOL.30: 3 residues within 4Å: Chain F: W.152, H.156, P.312 No protein-ligand interaction detected (PLIP) GOL.31: 6 residues within 4Å: Chain A: R.227, K.235 Chain F: A.69, L.70, E.71, R.262 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:L.70 Water bridges: F:G.254 GOL.32: 4 residues within 4Å: Chain E: E.65 Chain F: H.190, S.191, A.194 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.191, E:E.65 Water bridges: E:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egea, P.F. et al., Structures of the Signal Recognition Particle Receptor from the Archaeon Pyrococcus furiosus: Implications for the Targeting Step at the Membrane. Plos One (2008)

Release Date

2008-11-11

Peptides

Signal recognition particle receptor: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
C

E
A

F
C

Signal recognition particle receptor

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