SMTL ID : 3mk2.1

Placental alkaline phosphatase complexed with Phe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 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.14: 1 residues within 4Å: Chain B: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: W.248, N.249, E.252, L.284 No protein-ligand interaction detected (PLIP)

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.3: 10 residues within 4Å: Chain A: D.91, S.92, F.107, R.166, D.316, H.317, H.320, E.429, H.432 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:D.91, A:F.107 Salt bridges: A:H.153, A:R.166, A:H.317, A:H.320 PHE.4: 8 residues within 4Å: Chain A: R.250, L.253, M.254, S.257, E.290, E.293, A.294, R.297 10 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: F.4, F.4, A:E.290, A:E.293, A:E.293 Hydrophobic interactions: A:L.253, A:M.254, A:E.290, A:A.294 Salt bridges: A:R.250 PHE.16: 10 residues within 4Å: Chain B: D.91, S.92, F.107, R.166, D.316, H.317, H.320, E.429, H.432 Ligands: ZN.18 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:D.91, B:F.107 Salt bridges: B:H.153, B:R.166, B:H.317, B:H.320 PHE.17: 8 residues within 4Å: Chain B: R.250, L.253, M.254, S.257, E.290, E.293, A.294, R.297 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.253, B:M.254, B:E.290, B:A.294 Hydrogen bonds: B:E.293, F.17, F.17 Salt bridges: B:R.250

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: S.92, D.316, H.320, H.432 Ligands: PHE.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.316, A:D.316, A:H.320, A:H.432 ZN.6: 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.18: 5 residues within 4Å: Chain B: S.92, D.316, H.320, H.432 Ligands: PHE.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.316, B:D.316, B:H.320, B:H.432 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 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.1, H2O.2, H2O.3 MG.20: 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.22, H2O.23, H2O.24

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.10 CA.21: 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.31

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

ACT.9: 4 residues within 4Å: Chain A: A.378, G.380, K.381, A.387 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.378, A:G.380 Salt bridges: A:K.381 ACT.10: 4 residues within 4Å: Chain A: E.277, I.278, R.280, S.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.278 Water bridges: A:S.282 Salt bridges: A:R.280 ACT.11: 6 residues within 4Å: Chain A: F.208, N.232, V.234, Q.235, L.238, Y.246 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.246 Hydrogen bonds: A:N.232 ACT.22: 4 residues within 4Å: Chain B: A.378, G.380, K.381, A.387 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.378, B:G.380 Salt bridges: B:K.381 ACT.23: 4 residues within 4Å: Chain B: E.277, I.278, R.280, S.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.278 Water bridges: B:S.282 Salt bridges: B:R.280 ACT.24: 6 residues within 4Å: Chain B: F.208, N.232, V.234, Q.235, L.238, Y.246 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.246 Hydrogen bonds: B:N.232

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain A: Y.217, Q.223, E.270, P.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.270 Water bridges: A:Y.217, A:D.220, A:K.275 GOL.13: 3 residues within 4Å: Chain A: G.211, P.213, Y.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.211 GOL.25: 4 residues within 4Å: Chain B: Y.217, Q.223, E.270, P.271 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.217, B:E.270 Water bridges: B:K.275 GOL.26: 3 residues within 4Å: Chain B: G.211, P.213, Y.221 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.211

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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