SMTL ID : 6giz.1

PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - SUBSTRATE COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

2 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: 9 residues within 4Å: Chain A: G.70, L.107, Y.108, P.109, F.110, E.111, L.113, N.115, I.265 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.180, M.411, F.466, Q.487 Ligands: PEG.19 No protein-ligand interaction detected (PLIP)

2 x FE: FE (III) ION(Non-covalent)

FE.3: 7 residues within 4Å: Chain A: D.174, D.201, Y.204, H.377, H.379 Ligands: FE.4, PO4.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.174, A:D.201, A:Y.204, A:H.379, H2O.1 FE.4: 7 residues within 4Å: Chain A: D.174, D.201, N.258, H.340, H.377 Ligands: FE.3, PO4.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.201, A:H.340, A:H.377, H2O.1

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

NAG.5: 3 residues within 4Å: Chain A: L.209, N.211, T.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.213 Water bridges: A:N.211 NAG.6: 3 residues within 4Å: Chain A: N.267, T.269, F.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.267 Water bridges: A:Q.263 NAG.7: 5 residues within 4Å: Chain A: E.363, F.388, N.389, T.442 Ligands: PGE.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.363 Hydrogen bonds: A:N.389 Water bridges: A:R.358, A:R.358, A:R.358, A:N.389, A:N.389 NAG.8: 6 residues within 4Å: Chain A: C.422, N.440, G.448, S.449, F.450, C.451 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.440, A:F.450, A:C.451 NAG.9: 5 residues within 4Å: Chain A: K.474, N.475, T.477, H.478, Y.499 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.499 Water bridges: A:N.475, A:E.476

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

PO4.10: 11 residues within 4Å: Chain A: D.174, D.201, Y.204, N.258, H.259, H.350, H.377, H.379, E.409 Ligands: FE.3, FE.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.258, A:N.258, A:H.377, A:E.409 Salt bridges: A:H.259, A:H.350, A:H.377, A:H.379 PO4.11: 3 residues within 4Å: Chain A: S.311, K.312, S.313 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.313, A:S.313, A:S.313 Water bridges: A:K.312, A:K.312 PO4.12: 5 residues within 4Å: Chain A: A.349, K.410, A.412, T.413, T.414 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.411, A:T.413, A:T.414, A:T.414 Water bridges: A:A.349 Salt bridges: A:K.410

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 3 residues within 4Å: Chain A: P.162, R.163, E.476 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.163, A:R.163, A:R.163 PGE.14: 7 residues within 4Å: Chain A: E.283, S.284, E.285, W.319, K.322, D.323, K.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.285, A:E.285, A:K.322, A:K.326 PGE.15: 11 residues within 4Å: Chain A: R.358, N.389, Y.390, T.391, F.439, N.440, F.441, T.442, S.443, G.444 Ligands: NAG.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.439 Water bridges: A:F.439, A:S.443

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 4 residues within 4Å: Chain A: Y.86, V.94, R.95, E.96 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.86, A:V.94, A:R.95, A:E.96 Water bridges: A:E.96 PEG.17: 6 residues within 4Å: Chain A: G.40, W.41, G.64, D.65, Q.67, L.75 No protein-ligand interaction detected (PLIP) PEG.18: 5 residues within 4Å: Chain A: K.134, Y.136, A.153, F.154, S.249 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.134, A:Y.136, A:Y.136 Water bridges: A:R.155, A:S.249 PEG.19: 1 residues within 4Å: Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP)

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.20: 2 residues within 4Å: Chain A: S.367, Y.368 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.368 EDO.21: 3 residues within 4Å: Chain A: R.163, S.164 Ligands: EDO.25 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.164 EDO.22: 6 residues within 4Å: Chain A: G.87, L.88, S.92, V.94, R.95, Y.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.88, A:R.95 EDO.23: 6 residues within 4Å: Chain A: P.445, A.446, S.449, C.451, W.452, D.453 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.449, A:S.449, A:D.453, A:D.453 EDO.24: 3 residues within 4Å: Chain A: P.131, G.132, T.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.132 Water bridges: A:T.133 EDO.25: 5 residues within 4Å: Chain A: G.161, P.162, R.163, S.164 Ligands: EDO.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.163, A:R.163 EDO.26: 5 residues within 4Å: Chain A: W.58, H.123, F.277, A.278, F.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.277, A:F.279 EDO.27: 2 residues within 4Å: Chain A: D.418, P.419 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.418, A:D.418 Water bridges: A:H.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faba-Rodriguez, R. et al., Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants. Plant Commun. (2022)

Release Date

2019-11-27

Peptides

Purple acid phosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Purple acid phosphatase

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