SMTL ID : 7yiw.1

The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (ALPL) at Acidic pH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-octamer

Ligands

16 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: 3 residues within 4Å: Chain B: W.272, N.273, E.276 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: W.272, N.273, T.275, E.276 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: W.272, N.273, E.276, V.306, T.307 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: K.409, K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain E: W.272, N.273, E.276 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain E: K.410, N.432, M.435 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain F: W.272, N.273, E.276 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain F: K.409, K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain G: W.272, N.273, E.276, V.306 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain G: K.409, K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain H: W.272, N.273, T.275, E.276 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain H: K.410, N.432, S.434, M.435 No protein-ligand interaction detected (PLIP)

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

NAG.17: 1 residues within 4Å: Chain A: N.142 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: R.303, N.304, N.305 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.142 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: R.303, N.304, N.305 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.142 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.305 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.142, Q.201 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain D: N.305 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain E: N.142 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain E: N.305 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain F: N.142, T.143, Q.201 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain F: R.303, N.304, N.305 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain G: N.142 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: R.303, N.305 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain H: N.142, E.197, Q.201 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain H: R.303, N.305 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 4 residues within 4Å: Chain A: D.62, H.173, T.175, E.334 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.62, A:H.173 MG.25: 4 residues within 4Å: Chain B: D.62, H.173, T.175, E.334 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.62, B:H.173, B:T.175 MG.31: 4 residues within 4Å: Chain C: D.62, H.173, T.175, E.334 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.62, C:T.175, C:E.334 MG.37: 6 residues within 4Å: Chain D: D.62, H.173, A.174, T.175, P.176, E.334 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.173, D:T.175, D:E.334 MG.43: 4 residues within 4Å: Chain E: D.62, H.173, T.175, E.334 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.62, E:H.173, E:T.175, E:E.334 MG.49: 5 residues within 4Å: Chain F: D.62, H.173, A.174, T.175, E.334 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.62, F:H.173, F:E.334 MG.55: 4 residues within 4Å: Chain G: D.62, H.173, T.175, E.334 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.62, G:H.173, G:E.334 MG.61: 4 residues within 4Å: Chain H: D.62, H.173, T.175, E.334 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.62, H:H.173, H:T.175, H:E.334

16 x ZN: ZINC ION(Non-covalent)

ZN.20: 6 residues within 4Å: Chain A: S.112, D.339, H.343, H.381, H.456 Ligands: ZN.22 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.339, A:D.339, A:H.343, A:H.456 ZN.22: 6 residues within 4Å: Chain A: D.62, S.112, D.339, D.380, H.381 Ligands: ZN.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.112, A:D.380, A:H.381 ZN.26: 5 residues within 4Å: Chain B: S.112, D.339, H.343, H.456 Ligands: ZN.28 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.339, B:D.339, B:H.343, B:H.456 ZN.28: 6 residues within 4Å: Chain B: D.62, S.112, D.339, D.380, H.381 Ligands: ZN.26 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.62, B:S.112, B:D.380, B:H.381 ZN.32: 5 residues within 4Å: Chain C: S.112, D.339, H.343, H.456 Ligands: ZN.34 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.339, C:D.339, C:H.343, C:H.456 ZN.34: 6 residues within 4Å: Chain C: D.62, S.112, D.339, D.380, H.381 Ligands: ZN.32 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.62, C:S.112, C:D.380, C:H.381 ZN.38: 6 residues within 4Å: Chain D: S.112, D.339, H.343, H.381, H.456 Ligands: ZN.40 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.339, D:D.339, D:H.343, D:H.456 ZN.40: 6 residues within 4Å: Chain D: D.62, S.112, D.339, D.380, H.381 Ligands: ZN.38 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.62, D:S.112, D:D.380, D:H.381 ZN.44: 5 residues within 4Å: Chain E: S.112, D.339, H.343, H.381, H.456 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.339, E:D.339, E:H.343, E:H.456 ZN.46: 5 residues within 4Å: Chain E: D.62, S.112, D.339, D.380, H.381 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:S.112, E:D.380, E:H.381 ZN.50: 5 residues within 4Å: Chain F: S.112, D.339, H.343, H.456 Ligands: ZN.52 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.339, F:D.339, F:H.343, F:H.456 ZN.52: 6 residues within 4Å: Chain F: D.62, S.112, D.339, D.380, H.381 Ligands: ZN.50 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.62, F:S.112, F:D.380, F:H.381 ZN.56: 5 residues within 4Å: Chain G: S.112, D.339, H.343, H.456 Ligands: ZN.58 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.339, G:D.339, G:H.343, G:H.456 ZN.58: 6 residues within 4Å: Chain G: D.62, S.112, D.339, D.380, H.381 Ligands: ZN.56 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.62, G:D.380, G:H.381 ZN.62: 4 residues within 4Å: Chain H: S.112, D.339, H.343, H.456 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.339, H:D.339, H:H.343, H:H.456 ZN.64: 5 residues within 4Å: Chain H: D.62, S.112, D.339, D.380, H.381 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.62, H:S.112, H:D.380, H:H.381

8 x CA: CALCIUM ION(Non-covalent)

CA.21: 5 residues within 4Å: Chain A: E.237, Y.238, F.292, E.293, D.308 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.237, A:F.292, A:E.293, A:D.308, A:D.308 CA.27: 4 residues within 4Å: Chain B: E.237, F.292, E.293, 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 CA.33: 5 residues within 4Å: Chain C: E.237, F.292, E.293, T.307, D.308 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.237, C:F.292, C:E.293, C:D.308, C:D.308 CA.39: 5 residues within 4Å: Chain D: E.237, F.292, E.293, T.307, D.308 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.237, D:E.237, D:F.292, D:D.308, D:D.308 CA.45: 4 residues within 4Å: Chain E: E.237, F.292, E.293, D.308 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.237, E:F.292, E:E.293, E:D.308, E:D.308 CA.51: 6 residues within 4Å: Chain F: E.237, W.272, F.292, E.293, T.307, D.308 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.237, F:F.292, F:D.308 CA.57: 6 residues within 4Å: Chain G: R.225, E.237, F.292, E.293, T.307, D.308 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.237, G:E.237, G:F.292, G:D.308, G:D.308 CA.63: 4 residues within 4Å: Chain H: E.237, F.292, E.293, D.308 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.237, H:E.237, H:F.292, H:E.293, H: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

2023-07-19

Peptides

Alkaline phosphatase, tissue-nonspecific isozyme: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

D
B

E
G

F
H

G
F

H
E

Alkaline phosphatase, tissue-nonspecific isozyme