SMTL ID : 7u6f.1

Mouse retromer (VPS26/VPS35/VPS29) heterotrimers

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: E.575, L.576, A.577, E.578, L.579 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.577, A:E.578, A:L.579 GOL.2: 5 residues within 4Å: Chain A: L.743, N.744, I.747, Q.748, L.777 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.744 GOL.5: 5 residues within 4Å: Chain A: N.37, K.38, L.39, M.40, V.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.39, A:M.40 GOL.15: 5 residues within 4Å: Chain B: P.158, D.159, V.160, K.184 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.159, B:V.160, B:K.184 GOL.16: 4 residues within 4Å: Chain B: V.277, R.285, Y.286, F.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.285 GOL.17: 5 residues within 4Å: Chain B: Y.157, K.182, H.186, D.189, Q.305 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.182, B:K.182, B:Q.305 Water bridges: B:H.186

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

SO4.3: 3 residues within 4Å: Chain A: R.54 Chain B: E.234 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.54 SO4.4: 3 residues within 4Å: Chain A: Y.100, A.101, G.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.101 SO4.14: 6 residues within 4Å: Chain B: Y.118, R.262, D.263, V.264, N.265, K.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.265, B:K.266

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

EDO.6: 6 residues within 4Å: Chain A: R.54, N.103, I.104, I.105 Chain B: E.234 Ligands: SO4.3 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: C.137, R.138, G.146, E.189, L.193 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: N.294 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: E.288, L.289, H.290 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: S.349, V.352, S.353, N.356 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: K.323, Y.368 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: L.97, Y.100, A.101 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: Q.155, C.156, T.157, R.158, N.159, I.160 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: A.155, T.156, Y.157, P.158, W.295 Ligands: GOL.15 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: K.38, H.39, Y.40, Y.147, D.148, L.149 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: Q.66, G.67, I.68, R.69, E.94, T.135, V.137 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: K.213, K.214, E.215, E.226, T.227, E.228 Ligand excluded by PLIP EDO.22: 10 residues within 4Å: Chain B: E.77, L.78, F.79, N.80, D.81, A.124, N.125, V.126, R.127 Ligands: EDO.27 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: I.216, 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, L.154, A.155, P.259, W.295, R.296 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain B: K.82 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain B: R.139 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: N.80, R.127 Ligands: EDO.22 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: K.214, T.225, T.227 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kendall, A.K. et al., Improved mammalian retromer cryo-EM structures reveal a new assembly interface. J.Biol.Chem. (2022)

Release Date

2022-10-12

Peptides

Vacuolar protein sorting-associated protein 35: A
Vacuolar protein sorting-associated protein 26A: B
Vacuolar protein sorting-associated protein 29: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D1

B
B3

C
B4

Vacuolar protein sorting-associated protein 35

Vacuolar protein sorting-associated protein 26A

Vacuolar protein sorting-associated protein 29

Related Entries With Identical Sequence