SMTL ID : 1o7d.1

The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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.1: 21 residues within 4Å: Chain A: T.31, Q.34, Y.40 Chain B: A.51, L.52, Y.55, L.58 Chain C: H.26, N.29, D.30, A.32, R.33, S.36, E.37, R.64, N.67 Chain D: S.232, G.233, W.235, V.236, R.237 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:S.36, D:S.232, D:S.232 Hydrophobic interactions: B:A.51

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

NAG-NAG.2: 5 residues within 4Å: Chain D: N.43, N.63, Q.64, L.68, W.123 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain D: N.90, A.93 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.93 NAG-NAG.4: 3 residues within 4Å: Chain B: P.38, Y.39 Chain D: N.164 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.84 Water bridges: A:N.84

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 12 residues within 4Å: Chain A: H.23, D.25, W.28, D.147, F.149, R.171, D.270 Chain B: W.42 Chain C: H.16, D.17 Chain D: Y.58 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:D.147, A:R.171, A:Y.212, D:Y.58, D:Y.58

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: H.23, D.25, D.147 Chain C: H.16 Ligands: TRS.6 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Metal complexes: C:H.16, A:H.23, A:D.25, A:D.147

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

SO4.8: 4 residues within 4Å: Chain A: G.2, Y.3, K.4, R.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.3, A:K.4 Salt bridges: A:R.141 SO4.9: 4 residues within 4Å: Chain E: G.25, P.26, E.27, T.28 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.27, E:T.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heikinheimo, P. et al., The Structure of Bovine Lysosomal Alpha-Mannosidase Suggests a Novel Mechanism for Low-Ph Activation. J.Mol.Biol. (2003)

Release Date

2003-03-20

Peptides

Lysosomal alpha-mannosidase: A
Lysosomal alpha-mannosidase: B
Lysosomal alpha-mannosidase: C
Lysosomal alpha-mannosidase: D
Lysosomal alpha-mannosidase: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Lysosomal alpha-mannosidase

Lysosomal alpha-mannosidase

Lysosomal alpha-mannosidase

Lysosomal alpha-mannosidase

Lysosomal alpha-mannosidase