SMTL ID : 5jg8.1

Crystal structure of human acid sphingomyelinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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: 5 residues within 4Å: Chain A: N.477, T.479, Q.480, Q.491, F.529 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: P.328, Y.329, N.460 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: D.126, N.352 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: P.328, Y.329, N.460 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 4 residues within 4Å: Chain A: T.245, R.246, N.292, H.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.246

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.4: 6 residues within 4Å: Chain B: N.477, T.479, Q.480, Q.491, F.529, G.534 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.479 NAG-NAG-MAN.5: 5 residues within 4Å: Chain B: L.94, Q.244, T.245, R.246, N.292 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.94 Hydrogen bonds: B:T.245, B:R.246

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain A: D.163, H.165, D.235, H.416 Ligands: ZN.9, ACT.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.163, A:H.165, A:D.235, A:H.416, ACT.10 ZN.9: 7 residues within 4Å: Chain A: D.163, D.235, N.275, H.382, H.414 Ligands: ZN.8, ACT.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.235, A:D.235, A:H.382, A:H.414, ACT.10 ZN.14: 6 residues within 4Å: Chain B: D.163, H.165, D.235, H.416 Ligands: ZN.15, ACT.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.163, B:H.165, B:D.235, B:H.416 ZN.15: 7 residues within 4Å: Chain B: D.163, D.235, N.275, H.382, H.414 Ligands: ZN.14, ACT.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.235, B:H.382, B:H.414

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 9 residues within 4Å: Chain A: D.163, H.165, D.235, N.275, H.276, H.414, H.416 Ligands: ZN.8, ZN.9 5 PLIP interactions: 5 interactions with chain A Salt bridges: A:H.165, A:H.239, A:H.276, A:H.414, A:H.416 ACT.16: 11 residues within 4Å: Chain B: D.163, H.165, D.235, H.239, N.275, H.276, H.382, H.414, H.416 Ligands: ZN.14, ZN.15 5 PLIP interactions: 5 interactions with chain B Salt bridges: B:H.165, B:H.239, B:H.276, B:H.414, B:H.416

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

NAG.11: 3 residues within 4Å: Chain A: G.40, N.43 Chain B: I.82 No protein-ligand interaction detected (PLIP) NAG.12: 6 residues within 4Å: Chain A: S.130, W.131, N.132, K.390, S.391, W.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.391 NAG.13: 2 residues within 4Å: Chain A: D.126, N.352 No protein-ligand interaction detected (PLIP) NAG.17: 3 residues within 4Å: Chain A: I.82 Chain B: F.39, N.43 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.43 NAG.18: 2 residues within 4Å: Chain B: W.131, N.132 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Z.J. et al., Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. J.Mol.Biol. (2016)

Release Date

2016-07-06

Peptides

Sphingomyelin phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sphingomyelin phosphodiesterase