SMTL ID : 3w81.1 (1 other biounit)

Human alpha-l-iduronidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1: 15 residues within 4Å: Chain A: C.27, P.28, P.29, L.30, P.31, H.32, W.280, S.281, F.326, Y.329, H.330, Q.344, N.346, V.468, F.469 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.330, A:R.342, A:Q.344 Water bridges: A:R.342

1 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: 3 residues within 4Å: Chain A: I.244, E.248, N.389 No protein-ligand interaction detected (PLIP)

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

NAG.3: 5 residues within 4Å: Chain A: R.74, N.84, T.86, H.87 Ligands: TLA.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.74, A:N.84 Water bridges: A:N.84, A:T.86

3 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 9 residues within 4Å: Chain A: L.14, W.15, N.305, A.309, Q.374, L.375, W.376, A.377, E.378 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.374, A:A.377 Water bridges: A:N.305, A:N.305, A:Q.374 TLA.5: 3 residues within 4Å: Chain A: R.18, R.19, R.22 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.18, A:R.19, A:R.22, A:R.22 Salt bridges: A:R.19, A:R.22 TLA.6: 6 residues within 4Å: Chain A: R.74, Y.83, N.84, F.85, R.136 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.85, A:R.136 Salt bridges: A:R.74, A:R.136

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: K.298, N.389, H.390, T.391, D.418, D.419, R.421 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.298, A:H.390, A:D.418, A:R.421 Water bridges: A:T.391, A:R.421

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain A: H.159, S.198, H.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.198, A:S.198, A:S.198 Salt bridges: A:H.159, A:H.200

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

CL.9: 5 residues within 4Å: Chain A: P.276, L.277, W.286, R.287, R.337 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maita, N. et al., Human alpha-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-08-21

Peptides

Alpha-L-iduronidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-L-iduronidase

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