SMTL ID : 5bro.1

Crystal structure of modified HexB (modB)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 6 residues within 4Å: Chain A: M.23, T.24, P.25, L.27, Y.138, N.148 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: E.94, N.100, Q.305 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain B: M.23, T.24, P.25, L.27, Y.138, N.148 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: E.94, N.100, Q.305 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: G.415, Q.416, D.417, W.418, P.462, R.463, Q.502, P.503, L.504 Chain B: Y.450 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.417, A:W.418, A:Q.502, A:Q.502, A:L.504 GOL.7: 10 residues within 4Å: Chain A: Y.450 Chain B: G.415, Q.416, D.417, W.418, P.462, R.463, Q.502, P.503, L.504 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.417, B:D.417, B:W.418, B:Q.502, B:Q.502, B:L.504

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 5 residues within 4Å: Chain A: Y.36, I.37, F.56, R.57, H.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.37 FMT.8: 5 residues within 4Å: Chain B: Y.36, I.37, F.56, R.57, H.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.37, B:H.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitakaze, K. et al., Protease-resistant modified human beta-hexosaminidase B ameliorates symptoms in GM2 gangliosidosis model. J.Clin.Invest. (2016)

Release Date

2016-05-04

Peptides

Beta-hexosaminidase subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-hexosaminidase subunit beta