SMTL ID : 1m01.2 (1 other biounit)

Wildtype Streptomyces plicatus beta-hexosaminidase in complex with product (GlcNAc)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 14 residues within 4Å: Chain A: R.168, H.256, D.319, E.320, W.350, W.367, Y.399, D.401, M.402, L.412, W.414, W.448, E.450 Ligands: GOL.6 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.319, A:W.350, A:W.367 Hydrogen bonds: A:R.168, A:R.168, A:H.256, A:D.319, A:D.319, A:E.320, A:D.401 Salt bridges: B:K.281 NAG.9: 14 residues within 4Å: Chain B: R.168, H.256, D.319, E.320, W.350, W.367, Y.399, D.401, M.402, L.412, W.414, W.448, E.450 Ligands: GOL.14 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.319, B:W.350, B:W.367 Hydrogen bonds: B:R.168, B:R.168, B:H.256, B:D.319, B:E.320, B:Y.399, B:D.401 Salt bridges: A:K.281

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

CL.2: 5 residues within 4Å: Chain A: Y.277, K.281 Chain B: L.412, S.413, W.414 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: D.181, R.182, R.185 Ligand excluded by PLIP CL.4: 7 residues within 4Å: Chain A: K.281, V.282 Chain B: K.281, V.282 Ligands: GOL.6, CL.12, GOL.14 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: L.412, S.413, W.414 Chain B: Y.277, K.281 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: D.181, R.182, R.185 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain A: K.281, V.282 Chain B: K.281, V.282 Ligands: CL.4, GOL.6, GOL.14 Ligand excluded by PLIP

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

SO4.5: 3 residues within 4Å: Chain A: R.156, Y.157, A.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.157 Water bridges: A:Y.157 Salt bridges: A:R.156 SO4.13: 3 residues within 4Å: Chain B: R.156, Y.157, A.429 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.157 Salt bridges: B:R.156

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 11 residues within 4Å: Chain A: V.282, E.320, W.414 Chain B: K.281, V.282, G.283, F.284 Ligands: NAG.1, CL.4, GOL.7, CL.12 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.281, B:V.282, B:V.282, A:E.320, A:W.414 Water bridges: B:V.282, B:G.283, A:E.320 GOL.7: 9 residues within 4Å: Chain A: H.351, Q.352, W.367, E.376, W.414 Chain B: F.284, H.322, S.323 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.351, A:Q.352, A:E.376 Water bridges: A:R.371 GOL.8: 6 residues within 4Å: Chain A: R.371, A.415, G.416 Chain B: D.270, V.272, P.274 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.270, A:R.371, A:A.415 Water bridges: B:D.270, B:V.272, A:D.370, A:D.396, A:Y.417, A:R.422 GOL.14: 11 residues within 4Å: Chain A: K.281, V.282, G.283, F.284 Chain B: V.282, E.320, W.414 Ligands: CL.4, NAG.9, CL.12, GOL.15 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.281, A:V.282, A:V.282, B:W.414 Water bridges: A:V.282, A:G.283, B:E.320 GOL.15: 9 residues within 4Å: Chain A: F.284, H.322, S.323 Chain B: H.351, Q.352, W.367, E.376, W.414 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.351, B:Q.352, B:E.376 Water bridges: B:R.371 GOL.16: 6 residues within 4Å: Chain A: D.270, V.272, P.274 Chain B: R.371, A.415, G.416 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.371, B:A.415, A:D.270 Water bridges: B:Y.417, B:R.422, A:D.270, A:D.270, A:V.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, S.J. et al., Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. J.Biol.Chem. (2002)

Release Date

2003-01-21

Peptides

Beta-N-acetylhexosaminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-N-acetylhexosaminidase

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