SMTL ID : 6rrn.1

GOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: R.164, N.165, L.168, M.421, V.424, R.425, V.949 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.165 Water bridges: A:R.164, A:E.428, A:R.951 EDO.2: 5 residues within 4Å: Chain A: K.51, Y.255, H.261, P.267, W.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.51 Water bridges: A:Q.52, A:Q.52 EDO.3: 6 residues within 4Å: Chain A: D.30, V.31, Q.32, E.35, L.36, R.39 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.32, A:Q.32 Water bridges: A:D.30, A:Q.230, A:Q.230 EDO.5: 6 residues within 4Å: Chain A: W.433, R.952, Q.961, L.991, P.992, H.1031 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.433, A:R.952, A:R.952 EDO.7: 7 residues within 4Å: Chain A: M.33, L.34, Y.37, D.391, I.802, K.803, R.804 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.391, A:D.391, A:K.803, A:R.804 Water bridges: A:L.34, A:K.803, A:R.805 EDO.8: 9 residues within 4Å: Chain A: Y.37, F.42, H.218, F.393, T.394, Y.402, L.810, A.814, Y.817 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.394, A:T.394, A:Y.817 EDO.9: 6 residues within 4Å: Chain A: R.216, Y.255, S.256, Y.395, D.397, W.403 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.216, A:R.216, A:S.256, A:D.397, A:D.397 Water bridges: A:Y.255, A:Y.257

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.4: 5 residues within 4Å: Chain A: S.522, R.528, Y.560, R.605, Q.754 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.522, A:Y.560, A:Q.754 Water bridges: A:S.517, A:S.522, A:D.558, A:R.605, A:R.605, A:R.765, A:R.765 Salt bridges: A:R.528, A:R.605, A:R.765

1 x KFT: (2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-~{N}-pentyl-pyrrolidine-2-carboxamide(Non-covalent)

KFT.6: 14 residues within 4Å: Chain A: H.78, D.80, W.83, D.192, F.194, R.216, Y.257, D.329, H.459, D.460, Y.715, R.864, G.865 Ligands: ZN.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.83 Hydrogen bonds: A:R.216, A:Y.257, A:D.329, A:T.465, A:T.465, A:Y.715 Water bridges: A:R.216, A:D.329

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain A: H.78, D.80, D.192, H.459 Ligands: KFT.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:D.80, A:D.192, A:H.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Armstrong, Z. et al., Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J.Am.Chem.Soc. (2020)

Release Date

2020-07-08

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

Related Entries With Identical Sequence