SMTL ID : 6sni.1

Cryo-EM structure of nanodisc reconstituted yeast ALG6 in complex with 6AG9 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

5 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 7 residues within 4Å: Chain A: N.494, V.496, W.497, F.500, I.542, L.545, Y.549 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.500, A:L.545, A:Y.549 PTY.2: 3 residues within 4Å: Chain A: V.495, S.499, V.535 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.535 Hydrogen bonds: A:S.499, A:S.499 PTY.3: 3 residues within 4Å: Chain A: S.499, G.503, A.507 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.507 PTY.4: 5 residues within 4Å: Chain A: F.61, I.169, I.177, Y.178 Ligands: PTY.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.61, A:I.169, A:I.177, A:Y.178 PTY.5: 8 residues within 4Å: Chain A: F.171, P.174, Y.178, Y.227, N.230, N.231, D.234 Ligands: PTY.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.171, A:P.174, A:Y.178 Hydrogen bonds: A:N.230, A:N.231

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 10 residues within 4Å: Chain A: L.255, Y.256, P.259, F.262, S.353, T.357, M.365, F.388, S.392 Ligands: Y01.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.256, A:P.259, A:F.262, A:F.388, A:F.388 Hydrogen bonds: A:T.357 Y01.7: 7 residues within 4Å: Chain A: I.248, F.295, L.305, I.308, H.309 Chain B: N.31, Y.33 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.248, A:F.295, A:L.305, A:I.308 Salt bridges: A:H.309 Hydrogen bonds: B:N.31, B:Y.33 Y01.8: 7 residues within 4Å: Chain A: L.255, F.318, A.319, Q.350 Chain B: W.106, Y.107 Ligands: Y01.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.255, B:W.106 Hydrogen bonds: A:A.319, A:Q.350, B:Y.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bloch, J.S. et al., Structure and mechanism of the ER-based glucosyltransferase ALG6. Nature (2020)

Release Date

2020-03-11

Peptides

Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase: A
6AG9-Fab heavy chain: B
6AG9-Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
H

C
L

Membrane

We predict this structure to be a membrane protein.
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Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase

6AG9-Fab heavy chain

6AG9-Fab light chain

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