SMTL ID : 4fdi.1

The molecular basis of mucopolysaccharidosis IV A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.176, N.178 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.176, A:E.176 Water bridges: A:N.178, A:N.178, A:N.178 NAG.2: 3 residues within 4Å: Chain A: N.397, S.399 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.397 NAG.6: 2 residues within 4Å: Chain B: E.176, N.178 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.176, B:E.176 Water bridges: B:N.178, B:N.178 NAG.7: 4 residues within 4Å: Chain A: N.397 Chain B: N.397, S.399 Ligands: NAG.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.397, A:N.397

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.13, D.14, A.53, D.262, N.263 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.13, A:D.14, A:D.262, A:D.262 CA.8: 6 residues within 4Å: Chain B: D.13, D.14, A.53, D.262, N.263 Ligands: CIT.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.13, B:D.14, B:D.262, B:D.262

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 6 residues within 4Å: Chain A: L.52, A.53, Y.82, H.210, K.284, Q.285 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.82 Hydrogen bonds: A:Y.82, A:Y.82, A:K.284 Water bridges: A:K.284, A:Q.285 Salt bridges: A:K.114, A:H.116, A:H.210, A:H.210, A:K.284, A:K.284 CIT.9: 8 residues within 4Å: Chain B: L.52, A.53, Y.82, C.139, H.210, K.284, Q.285 Ligands: CA.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.82, B:Y.82 Hydrogen bonds: B:K.284, B:Q.285 Water bridges: B:Y.82, B:K.284, B:Q.285 Salt bridges: B:K.114, B:H.116, B:H.210, B:H.210, B:K.284, B:K.284, B:K.284

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: L.364, F.376, W.377, V.446, Q.450 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.364, A:Q.450 GOL.10: 5 residues within 4Å: Chain B: L.364, F.376, W.377, V.446, Q.450 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.364, B:Q.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rivera-Colon, Y. et al., The Structure of Human GALNS Reveals the Molecular Basis for Mucopolysaccharidosis IV A. J.Mol.Biol. (2012)

Release Date

2012-09-05

Peptides

N-acetylgalactosamine-6-sulfatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylgalactosamine-6-sulfatase

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