SMTL ID : 5wrv.1

Complex structure of human SRP72/SRP68

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

ACT.1: 4 residues within 4Å: Chain A: K.98 Chain B: D.44, V.45, T.46 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.45 Hydrogen bonds: B:V.45, B:T.46 Salt bridges: A:K.98 ACT.6: 2 residues within 4Å: Chain A: L.87 Chain B: Q.57 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.87 Water bridges: B:Q.57, B:Q.57, B:Q.57

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: F.83, D.84, L.85, N.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.84 GOL.7: 4 residues within 4Å: Chain B: I.101, Q.107, K.112, Y.115 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain A: A.91, F.92 Chain B: G.22, Q.23, F.27 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.23, A:F.92 Water bridges: B:N.19, B:Q.23, B:Q.57 GOL.9: 1 residues within 4Å: Chain B: R.121 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.121 Water bridges: B:Y.89, B:Y.89, B:R.90, B:R.90, B:R.90, B:R.90 GOL.10: 4 residues within 4Å: Chain A: L.99 Chain B: S.16, N.19, R.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.16, B:N.19

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

SO4.3: 8 residues within 4Å: Chain B: N.77, N.78, S.79, L.80, S.81, A.104, N.105, Q.106 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.79, B:S.79, B:S.81, B:S.81, B:N.105, B:Q.106 Water bridges: B:F.82, B:Q.106 SO4.4: 4 residues within 4Å: Chain B: S.60, F.61, K.62, E.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.60, B:K.62, B:E.63 Water bridges: B:F.61, B:F.61

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: F.83, L.85 Chain B: E.113, Q.117, Y.132, N.150 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.113, B:Q.117, B:Y.132, B:N.150, A:L.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Human apo-SRP72 and SRP68/72 complex structures reveal the molecular basis of protein translocation. J Mol Cell Biol (2017)

Release Date

2017-06-21

Peptides

Signal recognition particle subunit SRP68: A
Signal recognition particle subunit SRP72: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Signal recognition particle subunit SRP68

Signal recognition particle subunit SRP72

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