SMTL ID : 6git.1

PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - PRODUCT COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 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: 5 residues within 4Å: Chain A: 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, PO4.10 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, PO4.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.201, A:H.340, A:H.377

6 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.115 Water bridges: A:F.110, A:L.113 NAG.5: 6 residues within 4Å: Chain A: R.18, R.21, N.180, M.411, F.466 Ligands: EDO.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.466 Hydrogen bonds: A:R.18, A:N.180 Water bridges: A:R.18, A:N.180 NAG.6: 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.7: 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, A:T.269 NAG.8: 5 residues within 4Å: Chain A: E.363, F.388, N.389, T.442 Ligands: 1PE.19 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.363 Hydrogen bonds: A:N.389, A:T.442 Water bridges: A:R.358, A:R.358, A:R.358, A:N.389, A:N.389 NAG.9: 6 residues within 4Å: Chain A: C.422, N.440, G.448, S.449, F.450, C.451 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.440, A:F.450, A:C.451 Water bridges: A:S.449, A:S.449

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

PO4.10: 12 residues within 4Å: Chain A: D.174, D.201, Y.204, N.258, H.259, H.340, H.350, H.377, H.379, E.409 Ligands: FE.2, FE.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: 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: 6 residues within 4Å: Chain A: K.348, A.349, K.410, A.412, T.413, T.414 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:M.411, A:T.413, A:T.414, A:T.414, A:T.414 Water bridges: A:K.348, A:A.349, A:M.411 Salt bridges: A:K.410

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

PEG.12: 7 residues within 4Å: Chain A: G.40, W.41, G.64, D.65, F.66, Q.67, L.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.41, A:D.65 PEG.13: 5 residues within 4Å: Chain A: V.185, A.189, Y.242, P.245, V.246 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.242, A:S.249 PEG.14: 6 residues within 4Å: Chain A: Q.192, P.193, D.194, S.249, T.250 Ligands: PGE.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.194, A:S.249 PEG.15: 1 residues within 4Å: Chain A: A.159 No protein-ligand interaction detected (PLIP) PEG.16: 7 residues within 4Å: Chain A: P.445, A.446, S.449, C.451, W.452, D.453, R.454 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.449, A:D.453, A:R.454

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

PGE.17: 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 PGE.18: 7 residues within 4Å: Chain A: K.134, Y.136, A.153, F.154, R.155, S.249 Ligands: PEG.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.134, A:Y.136, A:Y.136, A:R.155

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.19: 12 residues within 4Å: Chain A: R.352, R.358, N.389, Y.390, T.391, F.439, N.440, F.441, T.442, S.443, G.444 Ligands: NAG.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.443, A:G.444 Water bridges: A:T.442, A:S.443

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

EDO.20: 6 residues within 4Å: Chain A: Y.86, R.95, E.96, Q.127 Ligands: EDO.30, EDO.31 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.86, A:R.95, A:E.96, A:Q.127 EDO.21: 2 residues within 4Å: Chain A: S.367, Y.368 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.368, A:Y.368 EDO.22: 7 residues within 4Å: Chain A: R.168, N.191, I.470, E.472, K.482, H.484 Ligands: EDO.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.482, A:K.482, A:H.484 EDO.23: 2 residues within 4Å: Chain A: R.21 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.21 EDO.24: 4 residues within 4Å: Chain A: A.325, K.326, V.327, D.328 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.328 EDO.25: 4 residues within 4Å: Chain A: D.328, S.330, V.331 Ligands: EDO.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.330 EDO.26: 5 residues within 4Å: Chain A: R.168, S.190, N.191, Q.192 Ligands: EDO.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.168, A:Q.192 EDO.27: 2 residues within 4Å: Chain A: R.163, S.164 No protein-ligand interaction detected (PLIP) EDO.28: 2 residues within 4Å: Chain A: D.418, P.419 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.415, A:H.415, A:D.418, A:D.418 EDO.29: 1 residues within 4Å: Ligands: EDO.25 No protein-ligand interaction detected (PLIP) EDO.30: 6 residues within 4Å: Chain A: E.96, A.97, T.98, Q.127 Ligands: EDO.20, EDO.31 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.127, A:Q.127 EDO.31: 3 residues within 4Å: Chain A: E.96 Ligands: EDO.20, EDO.30 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.96, A:E.96

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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