SMTL ID : 7ou8.1

Human O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x 1XI: ~{N}-[(3~{Z},6~{S},7~{R},8~{R},8~{a}~{S})-7,8-bis(oxidanyl)-3-(phenylmethyl)imino-1,5,6,7,8,8~{a}-hexahydro-[1,3]thiazolo[3,4-a]pyridin-6-yl]ethanamide(Non-covalent)

1XI.1: 19 residues within 4Å: Chain A: G.156, F.157, Y.158, K.187, D.263, D.264, C.299, Y.303, W.307, T.331, V.335, I.336, W.358, N.360, V.363, D.365, Y.366, N.393, H.454 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.263, A:Y.303, A:W.307, A:T.331, A:V.335, A:W.358 Hydrogen bonds: A:G.156, A:K.187, A:D.263, A:D.263, A:D.263, A:Y.303, A:N.360, A:N.393 pi-Stacking: A:H.454 1XI.2: 19 residues within 4Å: Chain B: G.156, F.157, Y.158, K.187, D.263, D.264, C.299, Y.303, W.307, T.331, V.335, I.336, W.358, N.360, V.363, D.365, Y.366, N.393, H.454 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.263, B:Y.303, B:W.307, B:W.307, B:T.331, B:W.358 Hydrogen bonds: B:G.156, B:K.187, B:D.263, B:D.263, B:Y.303, B:N.360, B:N.393 pi-Stacking: B:H.454

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

EDO.3: 7 residues within 4Å: Chain B: Q.522, M.559, F.560, D.563, K.583, D.610, Y.611 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.583, B:D.610, B:D.610 Water bridges: B:F.560, B:F.560, B:D.610

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain B: E.53, A.54, E.82, D.85 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.53, B:E.82, B:D.85, B:D.85, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez-Cuesta, M. et al., Bicyclic Picomolar OGA Inhibitors Enable Chemoproteomic Mapping of Its Endogenous Post-translational Modifications. J.Am.Chem.Soc. (2022)

Release Date

2022-04-13

Peptides

O-GlcNAcase BT_4395: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

O-GlcNAcase BT_4395

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