SMTL ID : 7zlj.1

Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary complex with Dol25-P-C-Man and acceptor peptide, bound to CMT2-Fab and anti-Fab nanobody

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GLY- SER- TRP- ALA- LYS- TRP- SER: synthetic octapeptide WEHI 1886493(Non-covalent)

GLY-SER-TRP-ALA-LYS-TRP-SER.1: 18 residues within 4Å: Chain D: R.69, T.70, E.71, M.72, G.207, R.211, W.214, L.394, Y.395, S.398, E.400, R.471, K.473, M.558, P.576, Y.578, Y.632 Ligands: IZU.2 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.395, D:R.471, D:K.473, D:Y.578 Hydrogen bonds: D:R.69, D:T.70, D:E.71, D:R.211, D:E.400 pi-Cation interactions: D:K.473

1 x IZU: [(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl-[(3~{S},6~{E},10~{Z},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphinic acid(Non-covalent)

IZU.2: 26 residues within 4Å: Chain D: E.71, Y.75, R.211, L.218, W.262, F.264, F.267, F.270, C.274, H.375, I.376, I.379, L.380, Y.395, F.401, C.461, V.464, M.465, L.468, I.469, R.471, L.472, H.577, Y.578, E.579 Ligands: GLY-SER-TRP-ALA-LYS-TRP-SER.1 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:W.262, D:F.264, D:F.264, D:F.264, D:F.267, D:F.267, D:F.270, D:I.376, D:I.379, D:L.380, D:V.464, D:L.468, D:I.469, D:L.472 Hydrogen bonds: D:E.71, D:Y.75, D:R.211, D:Y.395, D:R.471, D:Y.578, D:E.579, D:E.579

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bloch, J.S. et al., Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase. Nat.Chem.Biol. (2023)

Release Date

2023-01-11

Peptides

CMT2-Fab heavy chain: A
Anti-Fab nanobody: B
CMT2-Fab light chain: C
C-mannosyltransferase dpy-19: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
K

C
L

D
A

Membrane

We predict this structure to be a membrane protein.
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CMT2-Fab heavy chain

Anti-Fab nanobody

CMT2-Fab light chain

C-mannosyltransferase dpy-19

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