SMTL ID : 5f0j.1

Structure of retromer VPS26-VPS35 subunits bound to SNX3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: R.46 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.46 SO4.2: 2 residues within 4Å: Chain A: A.93, G.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.94 Water bridges: A:S.39 SO4.13: 5 residues within 4Å: Chain B: Y.120, D.265, V.266, N.267, K.268 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.120, B:N.267, B:K.268 Salt bridges: B:K.268 SO4.29: 5 residues within 4Å: Chain C: F.51, R.75, Y.76, S.77 Ligands: SO4.30 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.76, C:S.77, C:R.123 Water bridges: C:T.52, C:T.52 Salt bridges: C:R.75, C:K.100 SO4.30: 6 residues within 4Å: Chain C: K.100, A.101, Q.105, I.114, R.123 Ligands: SO4.29 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.101, C:A.101 Salt bridges: C:K.100, C:R.123 SO4.31: 5 residues within 4Å: Chain C: V.38, S.39, N.40, P.41, K.124 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.40 Salt bridges: C:K.124

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: N.29, K.30, L.31, M.32, D.33 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.29, A:L.31, A:M.32, A:D.33, A:D.33 GOL.14: 5 residues within 4Å: Chain B: P.160, D.161, V.162, K.186 Ligands: EDO.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.161, B:V.162, B:K.186, B:K.186 GOL.15: 6 residues within 4Å: Chain B: Q.212, N.277, V.279, R.287, F.289, E.328 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.212, B:N.277, B:R.287, B:Q.291 GOL.16: 4 residues within 4Å: Chain B: Y.159, K.184, H.188, K.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.159, B:K.184, B:K.184 GOL.32: 4 residues within 4Å: Chain B: L.201, R.203, K.244 Chain C: S.31 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.203, C:S.31

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: R.46, I.97 Chain B: E.236, D.239 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: L.146, Q.147, R.150, T.214, V.217, R.218, Q.221 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: C.129, R.130, V.132, Q.133, R.142, E.181, K.184, L.185 Chain B: E.246 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: N.286, K.288 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: R.246, H.282 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: I.292, D.296, S.341, V.344, S.345, N.348, R.392 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: R.357, Y.360 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: L.35, A.93 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: K.112, N.151 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: T.158, P.160, W.297 Ligands: GOL.14 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: M.28, K.40, H.41, Y.42, Y.149, D.150 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: G.69, R.71, E.96, V.139 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: Y.123, K.215, E.217, E.228, E.230 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: E.79, L.80, F.81, N.82, A.126, N.127, V.128, R.129 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: I.218, G.220, D.265, K.269, F.270, S.271 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: E.121, Q.155, A.157, P.261, R.298 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: K.84 Ligands: EDO.26 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain B: R.141 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain B: N.82 Ligands: EDO.24 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: K.216, T.227, T.229 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: D.120, K.123 Chain C: T.13, R.15 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: F.51, T.53, R.73, R.75, D.78, I.154 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain A: R.196 Chain C: R.57 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain C: K.68, E.69 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucas, M. et al., Structural Mechanism for Cargo Recognition by the Retromer Complex. Cell (2016)

Release Date

2016-12-07

Peptides

Vacuolar protein sorting-associated protein 35: A
Vacuolar protein sorting-associated protein 26A: B
Sorting nexin-3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Vacuolar protein sorting-associated protein 35

Vacuolar protein sorting-associated protein 26A

Sorting nexin-3

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