SMTL ID : 6b9p.1

Structure of GH 38 Jack Bean alpha-mannosidase in complex with a 36-valent iminosugar cluster inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1: 29 residues within 4Å: Chain A: T.31, Q.34, A.342, Y.346, M.349, F.374, H.396, N.399, D.400, A.402, K.403, A.406, I.407, S.410, H.443, L.444, N.446, K.518, A.519, Y.520, E.521, G.522, V.799, C.800, M.801, T.811, R.813 Chain B: F.234, D.235 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.520, A:Q.34, A:H.396, A:K.403 Water bridges: B:D.235, A:Y.520, A:Y.520, A:E.521 Hydrophobic interactions: A:A.342 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3: 29 residues within 4Å: Chain A: F.234, D.235 Chain B: T.31, Q.34, A.342, Y.346, M.349, F.374, H.396, N.399, D.400, A.402, K.403, A.406, I.407, H.443, L.444, N.446, K.518, A.519, Y.520, E.521, G.522, Q.798, V.799, C.800, M.801, T.811, R.813 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.34, B:H.396, B:D.400, B:K.403 Water bridges: B:E.40, B:H.396, B:L.343, B:Y.346, B:Y.346, B:H.443, B:Y.520 Hydrophobic interactions: B:A.342

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.2: 1 residues within 4Å: Chain A: N.312 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.312 No protein-ligand interaction detected (PLIP)

2 x D0J: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{9-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]nonyl}piperidine-3,4,5-triol(Non-covalent)

D0J.5: 16 residues within 4Å: Chain A: H.23, D.25, W.28, D.145, F.147, R.170, Y.210, D.268, W.333, H.386, D.387, Y.625, G.788, R.789, G.790 Ligands: ZN.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.170, A:D.387 Water bridges: A:R.170, A:G.788 Salt bridges: A:D.145, A:D.268 D0J.7: 16 residues within 4Å: Chain B: H.23, D.25, W.28, D.145, F.147, R.170, Y.210, D.268, W.333, H.386, D.387, Y.625, G.788, R.789, G.790 Ligands: ZN.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.170, B:Y.210, B:D.387, B:Y.625 Water bridges: B:R.170, B:D.786, B:G.788 Salt bridges: B:D.145, B:D.268

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.23, D.25, D.145, H.386 Ligands: D0J.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.23, A:D.25, A:D.145, A:H.386 ZN.8: 5 residues within 4Å: Chain B: H.23, D.25, D.145, H.386 Ligands: D0J.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.23, B:D.25, B:D.145, B:H.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Howard, E. et al., Structural Basis of Outstanding Multivalent Effects in Jack Bean alpha-Mannosidase Inhibition. Angew. Chem. Int. Ed. Engl. (2018)

Release Date

2018-09-26

Peptides

Alpha-mannosidase from Canavalia ensiformis (jack bean): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-mannosidase from Canavalia ensiformis (jack bean)