SMTL ID : 5f0p.1

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 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: 4 residues within 4Å: Chain A: S.39, A.93, G.94 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.39, A:G.94 SO4.13: 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:K.266 Salt bridges: B:K.266 SO4.28: 7 residues within 4Å: Chain C: F.51, T.52, R.75, Y.76, S.77, R.123 Ligands: SO4.29 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.76, C:S.77, C:R.123 Salt bridges: C:R.75 SO4.29: 6 residues within 4Å: Chain C: K.100, A.101, Q.105, I.114, R.123 Ligands: SO4.28 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 SO4.30: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: 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: 4 residues within 4Å: Chain A: R.246, Q.251, E.280, H.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.246, A:Q.251 GOL.14: 5 residues within 4Å: Chain B: P.158, D.159, V.160, K.184 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.159, B:V.160, B:K.184, B:K.184 GOL.26: 5 residues within 4Å: Chain B: L.199, V.200, R.201, K.242 Chain C: S.31 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:V.200, B:R.201, B:R.201, C:S.31

20 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 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.244 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: N.286, K.288, N.289 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: R.357, Y.360 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: L.35, V.90, A.93 Ligands: SO4.2 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: H.379, D.421, Y.422, R.425 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: H.67, K.112, N.151 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: R.196 Chain C: D.37, R.57 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: T.156, P.158, K.184, I.293, W.295 Ligands: GOL.14 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: M.26, H.39, Y.40, Y.147, D.148 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: Q.66, G.67, I.68, R.69, E.94, V.137 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: Y.121, K.213, E.215, E.226, E.228 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain B: E.77, L.78, F.79, N.80, G.123, A.124, N.125, V.126, R.127 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: I.216, G.218, D.263, K.267, F.268, S.269 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: Q.153, L.154, A.155, P.259, W.295, R.296 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: N.162, S.163 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: V.160, N.161, N.162 Ligands: EDO.22 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: Y.157, K.182, H.186 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: K.214, T.225 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain C: K.68, E.69 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.27: 4 residues within 4Å: Chain B: E.167, H.175 Chain D: H.15, H.17 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.15, D:H.17, B:E.167, B:H.175

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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