SMTL ID : 5f0l.1

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: A.93, G.94 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.94 SO4.2: 6 residues within 4Å: Chain A: L.35, K.36, S.39, L.89, A.93 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.39, A:S.39 SO4.3: 7 residues within 4Å: Chain A: L.268, Q.269, T.270, L.271, N.272, I.314, I.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.268, A:L.271, A:N.272, A:N.272 SO4.12: 6 residues within 4Å: Chain A: G.94, N.95 Chain B: E.208, K.232, Y.233, E.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.234 SO4.13: 5 residues within 4Å: Chain B: Y.118, D.263, V.264, N.265, K.266 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.118, B:N.265, B:K.266 SO4.14: 5 residues within 4Å: Chain B: P.158, D.159, V.160, K.184 Ligands: EDO.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.159, B:V.160, B:V.160 Salt bridges: B:K.184 SO4.15: 4 residues within 4Å: Chain B: Q.210, K.232, R.285 Chain D: L.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.210 Salt bridges: B:K.232, B:R.285 SO4.28: 6 residues within 4Å: Chain C: F.51, R.75, Y.76, S.77, R.123 Ligands: SO4.29 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.77, C:R.123 Salt bridges: C:R.75, C:K.100 SO4.29: 7 residues within 4Å: Chain C: K.100, A.101, F.102, Q.105, I.114, R.123 Ligands: SO4.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.101 Salt bridges: C:K.100, C:R.123 SO4.30: 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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.5: 3 residues within 4Å: Chain A: H.67, K.112, N.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.112 GOL.16: 4 residues within 4Å: Chain B: Y.157, K.182, H.186 Chain C: R.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.182, B:K.182 GOL.17: 6 residues within 4Å: Chain B: M.26, K.38, H.39, Y.40, Y.147, D.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.40, B:D.148 GOL.31: 4 residues within 4Å: Chain B: L.199, R.201, K.242 Chain C: S.31 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.201, C:S.31 GOL.32: 2 residues within 4Å: Chain C: K.68, E.69 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.68, C:E.69, C:E.69

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

EDO.6: 3 residues within 4Å: Chain A: N.286, K.288, D.338 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: R.246, E.280, H.282 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: I.292, D.296, S.345, N.348 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: R.357 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: A.180, K.184, Q.241 Chain C: Q.21, L.23, A.26 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: R.196 Chain C: R.57 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: R.46, R.137 Chain B: Q.205, E.234, D.237 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: A.155, T.156, I.293, W.295 Ligands: SO4.14, EDO.24 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: Q.66, G.67, R.69, E.94 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: Y.121, A.124, K.213, E.226, E.228 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: E.77, L.78, N.80, G.123, A.124, N.125, V.126, R.127 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain B: I.216, T.217, G.218, D.263, K.266, K.267, F.268, S.269 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: Q.153, A.155, P.259, W.295, R.296 Ligands: EDO.19 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: N.162, S.163 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain B: R.139 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: E.177, K.194, Y.196, S.245 Chain C: K.19 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain C: R.104, Q.105, L.106, F.108, R.109, D.111, G.113 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: T.53, R.73, D.78, I.154 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
Natural resistance-associated macrophage protein 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Vacuolar protein sorting-associated protein 35

Vacuolar protein sorting-associated protein 26A

Sorting nexin-3

Natural resistance-associated macrophage protein 2

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