SMTL ID : 5fcz.2 (1 other biounit)

Streptomyces plicatus N-acetyl-beta-hexosaminidase in complex with Thio-NAglucal (TNX)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x TNX: 1,5-anhydro-2-deoxy-2-(ethanethioylamino)-D-arabino-hex-1-enitol(Non-covalent)

TNX.1: 16 residues within 4Å: Chain A: R.168, D.197, H.256, V.282, D.319, E.320, W.350, W.367, Y.399, D.401, M.402, L.412, W.414, W.448, E.450 Chain B: K.281 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain A Water bridges: B:K.281, A:D.197, A:D.319 Hydrophobic interactions: A:D.319, A:W.350, A:W.367, A:W.448 Hydrogen bonds: A:R.168, A:R.168, A:D.319, A:D.319, A:D.401, A:W.414, A:E.450 TNX.13: 16 residues within 4Å: Chain A: K.281 Chain B: R.168, D.197, H.256, V.282, D.319, E.320, W.350, W.367, Y.399, D.401, M.402, L.412, W.414, W.448, E.450 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.319, B:W.350, B:W.367, B:W.448 Hydrogen bonds: B:R.168, B:R.168, B:D.319, B:D.401, B:W.414, B:E.450 Water bridges: B:D.197, B:D.319, A:K.281

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.156, Y.157, A.429, A.437 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.157 Water bridges: A:R.156, A:A.437 Salt bridges: A:R.156 SO4.3: 4 residues within 4Å: Chain A: R.58, T.79, A.80, H.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.80, A:H.81 Salt bridges: A:R.58, A:H.81 SO4.14: 4 residues within 4Å: Chain B: R.156, Y.157, A.429, A.437 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.157 Water bridges: B:R.156, B:A.437 Salt bridges: B:R.156 SO4.15: 4 residues within 4Å: Chain B: R.58, T.79, A.80, H.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.80, B:H.81 Salt bridges: B:R.58, B:H.81

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: H.351, Q.352, W.367, G.368, L.369, E.376, W.414 Chain B: F.284, H.322, S.323 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.351, A:Q.352, B:S.323 Water bridges: A:E.320, A:T.372 GOL.16: 10 residues within 4Å: Chain A: F.284, H.322, S.323 Chain B: H.351, Q.352, W.367, G.368, L.369, E.376, W.414 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.351, B:Q.352, A:S.323 Water bridges: B:T.372

16 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain A: Y.277, G.279, T.280, K.281 Chain B: L.412, S.413, W.414 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: D.181, R.182, R.185, I.501 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: K.281, V.282 Chain B: K.281, V.282 Ligands: CL.19 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.50, H.81, G.82 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: K.115, A.116, A.117, H.244 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: A.158, N.189, K.190, R.312 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.75 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: P.141 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain A: L.412, S.413, W.414 Chain B: Y.277, G.279, T.280, K.281 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: D.181, R.182, R.185, I.501 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: K.281, V.282 Chain B: K.281, V.282 Ligands: CL.7 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: R.50, H.81, G.82 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: K.115, A.116, A.117, H.244 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: A.158, N.189, K.190, R.312 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: R.75 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain B: P.141 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santana, A.G. et al., N-Acetyl glycals are tight-binding and environmentally insensitive inhibitors of hexosaminidases. Chem.Commun.(Camb.) (2016)

Release Date

2016-10-26

Peptides

B-N-acetylhexosaminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

B-N-acetylhexosaminidase

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