SMTL ID : 6gj2.1

PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - COMPLEX WITH INOSITOL HEXASULPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 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: 6 residues within 4Å: Chain A: E.1, K.474, N.475, T.477, H.478, Y.499 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.499

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

FE.2: 7 residues within 4Å: Chain A: D.174, D.201, Y.204, H.377, H.379 Ligands: FE.3, PO4.18 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.174, A:D.201, A:Y.204, A:H.379 FE.3: 7 residues within 4Å: Chain A: D.174, D.201, N.258, H.340, H.377 Ligands: FE.2, PO4.18 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.201, A:H.340, A:H.377

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

NAG.4: 7 residues within 4Å: Chain A: G.70, L.107, Y.108, P.109, L.113, N.115, I.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.115 Water bridges: A:Y.108 NAG.5: 4 residues within 4Å: Chain A: R.18, N.180, M.411, F.466 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.466 Hydrogen bonds: A:R.18, A:N.180 Water bridges: A:N.180 NAG.6: 4 residues within 4Å: Chain A: L.209, N.211, G.212, T.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.211, A:T.213, A:T.213 NAG.7: 5 residues within 4Å: Chain A: E.363, F.388, N.389, T.442 Ligands: PG4.19 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.363, A:F.388 Hydrogen bonds: A:N.389, A:T.442, A:T.442 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

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

PEG.9: 7 residues within 4Å: Chain A: R.155, Q.192, P.193, D.194, S.249, T.250 Ligands: PGE.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.155 Water bridges: A:T.250 PEG.10: 8 residues within 4Å: Chain A: V.103, Y.104, S.105, L.107, Q.264, I.265, K.268, A.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.105, A:K.268 Water bridges: A:V.103 PEG.11: 3 residues within 4Å: Chain A: P.162, R.163, E.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.163, A:R.163 PEG.12: 7 residues within 4Å: Chain A: P.445, A.446, S.449, C.451, W.452, D.453, R.454 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.449, A:D.453, A:D.453, A:R.454 PEG.13: 7 residues within 4Å: Chain A: Y.86, V.94, R.95, E.96, Q.127, G.128 Ligands: EDO.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.95, A:E.96

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

PGE.14: 9 residues within 4Å: Chain A: E.283, S.284, E.285, S.293, W.319, K.322, D.323, K.326 Ligands: EDO.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.323, A:K.326 PGE.15: 7 residues within 4Å: Chain A: K.134, Y.136, A.153, F.154, R.155, S.249 Ligands: PEG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.134 Water bridges: A:R.155 PGE.16: 7 residues within 4Å: Chain A: R.36, G.40, W.41, G.64, D.65, Q.67, L.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.65 PGE.17: 4 residues within 4Å: Chain A: W.58, R.125, M.282, E.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.125, A:Q.127 Water bridges: A:E.283

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

PO4.18: 12 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.2, FE.3, IHS.24 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.174, A:Y.204, A:N.258, A:H.340 Salt bridges: A:H.259, A:H.350, A:H.377, A:H.379

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.19: 12 residues within 4Å: Chain A: R.352, E.355, R.358, N.389, Y.390, T.391, F.439, N.440, F.441, S.443, G.444 Ligands: NAG.7 No protein-ligand interaction detected (PLIP)

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

EDO.20: 4 residues within 4Å: Chain A: V.83, R.85, E.96, T.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.96 EDO.21: 6 residues within 4Å: Chain A: S.286, Y.291, E.315, R.318, W.319, K.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.315 Water bridges: A:E.315 EDO.22: 8 residues within 4Å: Chain A: A.52, S.284, S.293, F.294, D.295, H.300, D.323 Ligands: PGE.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.293 EDO.23: 2 residues within 4Å: Chain A: E.96 Ligands: PEG.13 No protein-ligand interaction detected (PLIP)

1 x IHS: D-MYO-INOSITOL-HEXASULPHATE(Non-covalent)

IHS.24: 15 residues within 4Å: Chain A: N.206, L.207, C.217, Y.218, S.219, A.223, H.229, N.258, H.259, H.350, E.353, E.409, A.431, F.432 Ligands: PO4.18 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.206, A:Y.218, A:S.219, A:S.219, A:N.258, A:E.409, A:D.430, A:F.432 Salt bridges: A:H.229, A:H.229, A:H.229, A:H.259, A:H.259, A:H.350

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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