SMTL ID : 9sh5.1

The cryo-EM structure of human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with MLS-0038949

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: W.256, N.257, E.260 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: W.256, N.257, E.260 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.2: 1 residues within 4Å: Chain A: N.289 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.126, Q.185 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.126, Q.185 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.289 No protein-ligand interaction detected (PLIP)

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.4: 3 residues within 4Å: Chain A: K.215, N.216, R.229 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.215, A:N.216 Hydrogen bonds: A:N.216 NAG-FUC.8: 3 residues within 4Å: Chain B: K.215, N.216, R.229 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.215 Hydrogen bonds: B:N.216, B:N.216

2 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.5: 4 residues within 4Å: Chain A: K.394, N.416, S.418, M.419 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.6: 5 residues within 4Å: Chain B: K.393, K.394, N.416, S.418, M.419 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain A: D.46, H.157, T.159, E.318 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.46, A:T.159, A:E.318 MG.16: 4 residues within 4Å: Chain B: D.46, H.157, T.159, E.318 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.46, B:T.159, B:E.318

4 x ZN: ZINC ION(Non-covalent)

ZN.12: 5 residues within 4Å: Chain A: S.96, D.323, H.327, H.440 Ligands: 01.15 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.323, A:H.327, A:H.440 ZN.14: 5 residues within 4Å: Chain A: D.46, S.96, D.323, D.364, H.365 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.46, A:S.96, A:D.364, A:H.365 ZN.17: 5 residues within 4Å: Chain B: S.96, D.323, H.327, H.440 Ligands: 01.20 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.323, B:H.327, B:H.440 ZN.19: 5 residues within 4Å: Chain B: D.46, S.96, D.323, D.364, H.365 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.46, B:S.96, B:D.364, B:H.365

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 4 residues within 4Å: Chain A: E.221, F.276, E.277, D.292 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.221, A:E.221, A:F.276, A:E.277, A:D.292 CA.18: 4 residues within 4Å: Chain B: E.221, F.276, E.277, D.292 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.221, B:E.221, B:F.276, B:E.277, B:D.292

2 x 01: 2,5-dimethoxy-~{N}-quinolin-3-yl-benzenesulfonamide

01.15: 14 residues within 4Å: Chain A: D.95, S.96, H.157, R.170, D.280, Y.283, R.321, H.324, H.327, E.328, H.437, H.440 Chain B: Y.374 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.324, A:E.328 pi-Cation interactions: A:H.327 01.20: 14 residues within 4Å: Chain A: Y.374 Chain B: D.95, S.96, H.157, R.170, D.280, Y.283, R.321, H.324, H.327, E.328, H.437, H.440 Ligands: ZN.17 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.324, B:E.328 pi-Cation interactions: B:H.327 Hydrogen bonds: A:Y.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drevet Mulard, E. et al., TNAP dephosphorylates phosphocholine and phosphoethanolamine and participates in triglyceride transport from the liver to the bloodstream. To Be Published

Release Date

2025-11-05

Peptides

Alkaline phosphatase, tissue-nonspecific isozyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alkaline phosphatase, tissue-nonspecific isozyme