SMTL ID : 7obq.1

SRP-SR at the distal site conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain E: K.77, T.78, S.95, D.117 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.78, E:S.95 MG.4: 3 residues within 4Å: Chain F: K.114, T.115 Ligands: GNP.3 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.115 MG.6: 4 residues within 4Å: Chain G: S.431, D.454, D.519 Ligands: GNP.5 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.431

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 20 residues within 4Å: Chain E: L.72, C.73, D.74, S.75, G.76, K.77, T.78, L.79, T.92, Q.93, T.94, S.95, G.120, N.180, K.181, D.183, S.247, A.248, K.249 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:D.74, E:D.74, E:S.75, E:G.76, E:T.78, E:L.79, E:T.92, E:T.94, E:S.95, E:G.120, E:N.180, E:K.181, E:S.247, E:A.248 Salt bridges: E:K.77, E:D.183 pi-Cation interactions: E:K.181

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.3: 22 residues within 4Å: Chain F: L.109, Q.110, G.111, G.113, K.114, T.115, T.116, K.120, D.138, R.141, Q.147, S.192, G.193, K.249, D.251, G.276, E.277 Chain G: N.426, G.427, R.457 Ligands: MG.4, GNP.5 20 PLIP interactions: 16 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:G.111, F:G.113, F:K.114, F:K.114, F:T.115, F:T.116, F:T.116, F:Q.147, F:Q.147, F:S.192, F:G.193, F:K.249, F:K.249, F:G.276, G:N.426, G:G.427, G:R.457 Salt bridges: F:D.251, F:E.277, G:R.457 GNP.5: 26 residues within 4Å: Chain F: Q.110, G.111, R.141, H.195 Chain G: N.426, V.428, G.429, K.430, S.431, T.432, N.433, K.436, D.454, R.457, Q.463, G.522, T.587, K.588, D.590, T.591, G.614, T.615, G.616, Q.617 Ligands: GNP.3, MG.6 23 PLIP interactions: 21 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:G.427, G:V.428, G:G.429, G:K.430, G:K.430, G:K.430, G:S.431, G:S.431, G:T.432, G:T.432, G:N.433, G:R.457, G:Q.463, G:G.522, G:T.587, G:K.588, G:K.588, G:G.616, G:Q.617, F:R.141 Salt bridges: G:D.590, F:R.141 pi-Cation interactions: G:K.588

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jomaa, A. et al., Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle. Cell Rep (2021)

Release Date

2021-07-21

Peptides

Signal recognition particle 19: B
EM14S01-3B_G0054400.mRNA.1.CDS.1: C
Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68: D
Signal recognition particle receptor subunit beta: E
Signal recognition particle 54 kDa protein: F
SRP receptor subunit alpha: G
Signal recognition particle subunit SRP72: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
q

C
s

D
u

E
v

F
x

G
y

H
z

Signal recognition particle 19

EM14S01-3B_G0054400.mRNA.1.CDS.1

Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68

Signal recognition particle receptor subunit beta

Signal recognition particle 54 kDa protein

SRP receptor subunit alpha

Signal recognition particle subunit SRP72

Related Entries With Identical Sequence