SMTL ID : 5f0m.1

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-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: 3 residues within 4Å: Chain A: Y.92, A.93, G.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.94 SO4.9: 5 residues within 4Å: Chain B: Y.118, D.263, V.264, N.265, K.266 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.118, B:N.265, B:N.265 Salt bridges: B:K.266 SO4.18: 6 residues within 4Å: Chain C: F.51, R.75, Y.76, S.77, R.123 Ligands: SO4.19 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.76, C:S.77, C:R.123 Salt bridges: C:R.75, C:K.100 SO4.19: 6 residues within 4Å: Chain C: K.100, A.101, Q.105, I.114, R.123 Ligands: SO4.18 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.101, C:A.101, C:Q.105 Salt bridges: C:K.100, C:R.123 SO4.20: 4 residues within 4Å: Chain C: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.31, A:M.32, A:D.33, A:D.33 GOL.4: 3 residues within 4Å: Chain A: K.112, C.148, N.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.112, A:Q.147, A:R.150 GOL.10: 4 residues within 4Å: Chain B: P.158, D.159, V.160, K.184 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.159, B:V.160, B:K.184, B:K.184 GOL.21: 5 residues within 4Å: Chain B: L.199, V.200, R.201, K.242 Chain C: S.31 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.31, B:V.200, B:R.201 GOL.22: 3 residues within 4Å: Chain C: L.67, K.68, E.69 No protein-ligand interaction detected (PLIP)

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

EDO.5: 4 residues within 4Å: Chain A: R.46, I.97 Chain B: E.234, D.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.46, A:I.97 EDO.6: 3 residues within 4Å: Chain A: R.246, E.280, H.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.246, A:E.280 EDO.7: 2 residues within 4Å: Chain A: S.48, H.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.48 EDO.8: 1 residues within 4Å: Chain A: R.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.357, A:R.357 EDO.11: 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 EDO.12: 3 residues within 4Å: Chain B: R.69, E.94, V.137 No protein-ligand interaction detected (PLIP) EDO.13: 8 residues within 4Å: Chain B: E.77, L.78, F.79, N.80, A.124, N.125, V.126, R.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.80, B:A.124 EDO.14: 5 residues within 4Å: Chain B: I.216, D.263, K.267, F.268, S.269 No protein-ligand interaction detected (PLIP) EDO.15: 6 residues within 4Å: Chain B: Q.153, L.154, A.155, P.259, W.295, R.296 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.154, B:R.296 EDO.16: 1 residues within 4Å: Chain B: K.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.227 EDO.17: 3 residues within 4Å: Chain B: Y.157, K.182, H.186 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.157, B:K.182, B:H.186, C:R.14 EDO.23: 6 residues within 4Å: Chain C: R.104, L.106, F.108, R.109, D.111, G.113 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.105, C:F.108, C:R.109, C:D.111

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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