SMTL ID : 1m04.2 (1 other biounit)

Mutant Streptomyces plicatus beta-hexosaminidase (D313N) in complex with product (GlcNAc)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 13 residues within 4Å: Chain A: R.168, H.256, N.319, E.320, W.350, W.367, Y.399, D.401, M.402, L.412, W.414, W.448, E.450 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.319, A:W.350, A:W.367 Hydrogen bonds: A:R.168, A:R.168, A:H.256, A:N.319, A:Y.399 Water bridges: A:H.256, A:N.319 NAG.7: 13 residues within 4Å: Chain B: R.168, H.256, N.319, E.320, W.350, W.367, Y.399, D.401, M.402, L.412, W.414, W.448, E.450 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.319, B:W.350, B:W.367 Hydrogen bonds: B:R.168, B:R.168, B:H.256, B:N.319, B:Y.399, B:Y.399 Water bridges: B:H.256, B:N.319

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: 5 residues within 4Å: Chain A: K.281, V.282 Chain B: K.281, V.282 Ligands: CL.10 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: L.412, S.413, W.414 Chain B: Y.277, K.281 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: D.181, R.182, R.185 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: K.281, V.282 Chain B: K.281, V.282 Ligands: CL.4 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.157 Water bridges: A:R.156, A:Y.157, A:Y.157 Salt bridges: A:R.156 SO4.11: 3 residues within 4Å: Chain B: R.156, Y.157, A.429 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.157 Water bridges: B:R.156 Salt bridges: B:R.156

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: H.351, Q.352, W.367, E.376, W.414 Chain B: F.284, H.322, S.323 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.12: 8 residues within 4Å: Chain A: F.284, H.322, S.323 Chain B: H.351, Q.352, W.367, E.376, W.414 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.351, B:Q.352, B:E.376 Water bridges: B:R.371

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

2002-12-11

Peptides

Beta-N-acetylhexosaminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-N-acetylhexosaminidase

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