SMTL ID : 7yix.1

The Cryo-EM Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (ScFv) Complex.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

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: 3 residues within 4Å: Chain A: W.272, N.273, E.276 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: K.409, K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: W.272, N.273, T.275, E.276, V.306, T.307 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: K.409, K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: R.140, N.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.140, A:N.142 NAG.6: 1 residues within 4Å: Chain A: N.305 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: R.140, N.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.142 NAG.12: 1 residues within 4Å: Chain B: N.305 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.62, H.173, T.175, E.334 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.62 MG.13: 4 residues within 4Å: Chain B: D.62, H.173, T.175, E.334 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.62, B:T.175

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: D.339, H.343, H.381, H.456 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.339, A:D.339, A:H.343, A:H.456 ZN.10: 4 residues within 4Å: Chain A: S.112, D.339, D.380, H.381 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.339, A:D.380, A:D.380, A:H.381 ZN.14: 4 residues within 4Å: Chain B: D.339, H.343, H.381, H.456 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.339, B:D.339, B:H.343, B:H.456 ZN.16: 4 residues within 4Å: Chain B: D.62, S.112, D.380, H.381 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.62, B:D.380, B:H.381, B:H.381

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: E.237, F.292, E.293, D.308 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.237, A:E.237, A:F.292, A:E.293, A:D.308 CA.15: 5 residues within 4Å: Chain B: E.237, F.292, E.293, T.307, D.308 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.237, B:E.237, B:F.292, B:E.293, B:D.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Y. et al., The structural pathology for hypophosphatasia caused by malfunctional tissue non-specific alkaline phosphatase. Nat Commun (2023)

Release Date

2023-08-16

Peptides

Alkaline phosphatase, tissue-nonspecific isozyme: AB
scFv: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alkaline phosphatase, tissue-nonspecific isozyme

scFv

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