SMTL ID : 4kjg.1

Structure of Rat Intestinal Alkaline Phosphatase expressed in insect cell

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-NAG-NAG.1: 2 residues within 4Å: Chain A: N.281, A.284 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-NAG.2: 5 residues within 4Å: Chain B: E.216, W.248, N.249, N.281, A.284 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.216

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: S.92, D.316, H.320, H.432 Ligands: 4NP.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.316, A:D.316, A:H.320, A:H.432 ZN.4: 6 residues within 4Å: Chain A: D.42, S.92, D.316, D.357, H.358 Ligands: 4NP.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.42, A:S.92, A:D.357, A:H.358 ZN.10: 5 residues within 4Å: Chain B: S.92, D.316, H.320, H.432 Ligands: 4NP.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.316, B:D.316, B:H.320, B:H.432 ZN.11: 6 residues within 4Å: Chain B: D.42, S.92, D.316, D.357, H.358 Ligands: 4NP.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.42, B:S.92, B:D.357, B:H.358

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.42, S.92, H.153, S.155, E.311 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.42, A:S.155, H2O.7, H2O.8, H2O.8 MG.6: 5 residues within 4Å: Chain A: E.216, F.269, E.270, K.275, 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 MG.7: 2 residues within 4Å: Chain A: S.342, T.345 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.342, A:T.345, H2O.1 MG.12: 5 residues within 4Å: Chain B: D.42, S.92, H.153, S.155, E.311 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.42, B:E.311, H2O.8, H2O.8, H2O.8 MG.13: 5 residues within 4Å: Chain B: E.216, F.269, E.270, K.275, 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.11 MG.14: 2 residues within 4Å: Chain B: S.342, T.345 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.342, B:T.345, H2O.8, H2O.8, H2O.8

2 x 4NP: 4-NITROPHENYL PHOSPHATE(Non-covalent)

4NP.8: 9 residues within 4Å: Chain A: D.91, S.92, R.166, D.316, H.320, H.432 Chain B: Y.367 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91, A:S.429 pi-Cation interactions: A:K.108, A:H.320 4NP.15: 10 residues within 4Å: Chain A: Y.367 Chain B: D.91, S.92, R.166, D.316, H.320, S.429, H.432 Ligands: ZN.10, ZN.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.91, B:S.429

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

NAG.9: 3 residues within 4Å: Chain A: G.385, K.386, N.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.385 NAG.16: 5 residues within 4Å: Chain B: N.381, D.384, G.385, K.386, N.408 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.386 Hydrogen bonds: B:G.385, B:G.385, B:N.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, K. et al., Crystal structure of rat intestinal alkaline phosphatase - Role of crown domain in mammalian alkaline phosphatases. J.Struct.Biol. (2013)

Release Date

2013-10-16

Peptides

Intestinal-type alkaline phosphatase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Intestinal-type alkaline phosphatase 1

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