SMTL ID : 3mk1.1

Refinement of placental alkaline phosphatase complexed with nitrophenyl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 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: 1 residues within 4Å: Chain A: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: W.248, N.249, E.252, L.284 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: W.248, N.249, E.252, L.284 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: S.92, D.316, H.320, H.432 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.1 ZN.4: 5 residues within 4Å: Chain A: D.42, S.92, D.316, D.357, H.358 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.42, A:D.42, A:D.357, A:H.358 ZN.5: 4 residues within 4Å: Chain A: D.42, S.155, E.311 Ligands: MG.6 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.42, A:S.155, A:E.311, H2O.1, H2O.1, H2O.1 ZN.18: 4 residues within 4Å: Chain B: S.92, D.316, H.320, H.432 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.22 ZN.19: 5 residues within 4Å: Chain B: D.42, S.92, D.316, D.357, H.358 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.42, B:D.42, B:D.357, B:H.358 ZN.20: 4 residues within 4Å: Chain B: D.42, S.155, E.311 Ligands: MG.21 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.42, B:S.155, B:E.311, H2O.23, H2O.23, H2O.23

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.42, S.155, E.311 Ligands: ZN.5 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.42, A:S.155, A:E.311, H2O.1, H2O.1, H2O.1 MG.21: 4 residues within 4Å: Chain B: D.42, S.155, E.311 Ligands: ZN.20 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.42, B:S.155, B:E.311, H2O.23, H2O.23, H2O.23

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.1 CA.22: 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.22

6 x NPO: P-NITROPHENOL(Non-covalent)

NPO.8: 7 residues within 4Å: Chain A: D.91, S.92, F.107, Q.108, R.166, H.432 Chain B: Y.367 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.107, A:F.107 pi-Stacking: B:Y.367 NPO.9: 8 residues within 4Å: Chain A: R.250, L.253, M.254, S.257, E.290, E.293, A.294, R.297 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.290 Hydrogen bonds: A:R.250, A:E.290 Water bridges: A:E.290 NPO.10: 4 residues within 4Å: Chain A: G.211, P.213, P.218, Y.221 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.213, A:Y.221, A:Y.221 Hydrogen bonds: A:P.218 NPO.23: 7 residues within 4Å: Chain A: Y.367 Chain B: D.91, S.92, F.107, Q.108, R.166, H.432 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.107, B:F.107 pi-Stacking: A:Y.367 NPO.24: 8 residues within 4Å: Chain B: R.250, L.253, M.254, S.257, E.290, E.293, A.294, R.297 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.290 Hydrogen bonds: B:R.250 Water bridges: B:E.290 NPO.25: 4 residues within 4Å: Chain B: G.211, P.213, P.218, Y.221 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.213, B:Y.221, B:Y.221 Hydrogen bonds: B:P.218

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 4 residues within 4Å: Chain A: K.275, Y.276, H.279, R.314 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.276 Water bridges: A:R.314, A:R.314, A:R.314, A:R.314, A:R.326 Salt bridges: A:H.279, A:R.314 PO4.26: 4 residues within 4Å: Chain B: K.275, Y.276, H.279, R.314 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.276 Water bridges: B:R.314, B:R.314, B:R.314, B:R.314, B:R.326 Salt bridges: B:H.279, B:R.314

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

ACT.12: 1 residues within 4Å: Chain A: L.258 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.258 ACT.13: 3 residues within 4Å: Chain A: E.277, I.278, R.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.278, A:R.280 Water bridges: A:S.282 Salt bridges: A:R.280 ACT.14: 5 residues within 4Å: Chain A: F.208, N.232, V.234, L.238, Y.246 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.246 Hydrogen bonds: A:N.232 ACT.27: 1 residues within 4Å: Chain B: L.258 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.258 ACT.28: 3 residues within 4Å: Chain B: E.277, I.278, R.280 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.278, B:R.280 Water bridges: B:S.282 Salt bridges: B:R.280 ACT.29: 5 residues within 4Å: Chain B: F.208, N.232, V.234, L.238, Y.246 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.246 Hydrogen bonds: B:N.232

2 x NA: SODIUM ION(Non-functional Binders)

NA.15: 1 residues within 4Å: Chain A: N.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.165, A:W.168 Water bridges: A:N.119 NA.30: 1 residues within 4Å: Chain B: N.165 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.165 Water bridges: B:N.119, B:W.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stec, B. et al., Refined structures of placental alkaline phosphatase show a consistent pattern of interactions at the peripheral site. Acta Crystallogr.,Sect.F (2010)

Release Date

2011-01-19

Peptides

Alkaline phosphatase, placental type: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alkaline phosphatase, placental type

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