SMTL ID : 1zed.1

Alkaline phosphatase from human placenta in complex with p-nitrophenyl-phosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.122 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.122, A:N.122 NAG.2: 4 residues within 4Å: Chain A: W.248, N.249, E.252, L.284 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.284 Hydrogen bonds: A:N.249 Water bridges: A:W.248 NAG.10: 1 residues within 4Å: Chain B: N.122 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.122, B:N.122 NAG.11: 4 residues within 4Å: Chain B: W.248, N.249, E.252, L.284 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.284 Hydrogen bonds: B:N.249 Water bridges: B:W.248

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.316, H.320, H.432 Ligands: PO3.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.316, A:D.316, A:H.320, A:H.432, H2O.29 ZN.4: 6 residues within 4Å: Chain A: D.42, S.92, D.316, D.357, H.358 Ligands: PO3.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.42, A:D.42, A:S.92, A:D.357, A:H.358 ZN.12: 4 residues within 4Å: Chain B: D.316, H.320, H.432 Ligands: PO3.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.316, B:D.316, B:H.320, B:H.432, H2O.59 ZN.13: 6 residues within 4Å: Chain B: D.42, S.92, D.316, D.357, H.358 Ligands: PO3.16 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.42, B:D.42, B:S.92, B:D.357, B:H.358

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.42, S.155, E.311 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.42, A:S.155, A:E.311, H2O.2, H2O.3, H2O.6 MG.14: 3 residues within 4Å: Chain B: D.42, S.155, E.311 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.42, B:S.155, B:E.311, H2O.31, H2O.32, H2O.35

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: E.216, F.269, E.270, D.285 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.216, A:F.269, A:E.270, A:D.285, H2O.7 CA.15: 4 residues within 4Å: Chain B: E.216, F.269, E.270, D.285 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.216, B:F.269, B:E.270, B:D.285, H2O.36

2 x PO3: PHOSPHITE ION(Non-covalent)

PO3.7: 11 residues within 4Å: Chain A: D.42, D.91, S.92, H.153, R.166, D.316, H.358, H.432 Ligands: ZN.3, ZN.4, PNP.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.92 Water bridges: A:A.154 Salt bridges: A:R.166, A:H.358, A:H.432 PO3.16: 11 residues within 4Å: Chain B: D.42, D.91, S.92, H.153, R.166, D.316, H.358, H.432 Ligands: ZN.12, ZN.13, PNP.17 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.92, B:D.316 Water bridges: B:A.154, B:D.316, B:H.320, B:H.432, B:H.432 Salt bridges: B:R.166, B:H.358, B:H.432

4 x PNP: METHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER(Non-covalent)

PNP.8: 7 residues within 4Å: Chain A: D.91, F.107, Q.108, R.166, H.432 Chain B: Y.367 Ligands: PO3.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A pi-Stacking: B:Y.367 Hydrophobic interactions: A:F.107 PNP.9: 9 residues within 4Å: Chain A: R.250, L.253, M.254, S.257, M.289, E.290, E.293, A.294, R.297 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.293 Hydrogen bonds: A:R.250, A:E.290 Water bridges: A:E.293 PNP.17: 7 residues within 4Å: Chain A: Y.367 Chain B: D.91, F.107, Q.108, R.166, H.432 Ligands: PO3.16 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.107 pi-Stacking: A:Y.367 PNP.18: 9 residues within 4Å: Chain B: R.250, L.253, M.254, S.257, M.289, E.290, E.293, A.294, R.297 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.293 Hydrogen bonds: B:R.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Llinas, P. et al., Structural Studies of Human Placental Alkaline Phosphatase in Complex with Functional Ligands. J.Mol.Biol. (2005)

Release Date

2005-06-28

Peptides

Alkaline phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alkaline phosphatase

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