SMTL ID : 5fql.1

Insights into Hunter syndrome from the structure of iduronate-2- sulfatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

6 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 8 residues within 4Å: Chain A: R.85, N.90, S.92, Q.96, E.100, Y.126, E.405, L.406 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.406 NAG-NAG-FUC.2: 7 residues within 4Å: Chain A: Y.83, R.85, V.86, N.119, T.121, S.124, Y.126 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.124 NAG-NAG-FUC.4: 4 residues within 4Å: Chain A: L.486, N.488, S.490, D.491 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.12: 8 residues within 4Å: Chain B: R.85, N.90, S.92, Q.96, E.100, Y.126, E.405, L.406 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.406 NAG-NAG-FUC.13: 7 residues within 4Å: Chain B: Y.83, R.85, V.86, N.119, T.121, S.124, Y.126 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.124 NAG-NAG-FUC.15: 4 residues within 4Å: Chain B: L.486, N.488, S.490, D.491 No protein-ligand interaction detected (PLIP)

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.3: 3 residues within 4Å: Chain A: Q.297, N.300, S.301 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: D.232, G.233, N.509, N.512 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: Q.297, N.300, S.301 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: D.232, G.233, N.509, N.512 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 9 residues within 4Å: Chain A: D.20, D.21, A.59, R.63, K.110, H.204, D.309, H.310, K.322 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.20, A:D.21, A:D.309, A:H.310 CA.17: 9 residues within 4Å: Chain B: D.20, D.21, A.59, R.63, K.110, H.204, D.309, H.310, K.322 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.20, B:D.21, B:D.309, B:H.310

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

NAG.7: 3 residues within 4Å: Chain A: P.218, E.220, N.221 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.220 Hydrogen bonds: A:N.221 NAG.8: 1 residues within 4Å: Chain A: N.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.255 NAG.18: 3 residues within 4Å: Chain B: P.218, E.220, N.221 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.220 Hydrogen bonds: B:N.221 NAG.19: 1 residues within 4Å: Chain B: N.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255

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

CL.9: 5 residues within 4Å: Chain A: G.109, K.110, H.134, P.135, H.201 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: G.148, P.149, D.150, G.151, E.152, H.154 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: L.33, I.222, T.223, R.272, F.276 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: G.109, K.110, H.134, P.135, H.201 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain B: G.148, P.149, D.150, G.151, E.152, H.154 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain B: L.33, I.222, T.223, R.272, F.276 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demydchuk, M. et al., Insights into Hunter syndrome from the structure of iduronate-2-sulfatase. Nat Commun (2017)

Release Date

2017-01-18

Peptides

IDURONATE-2-SULFATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

IDURONATE-2-SULFATASE