SMTL ID : 3zk4.1

Structure of purple acid phosphatase PPD1 isolated from yellow lupin (Lupinus luteus) seeds

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-hexamer

Ligands

12 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: 4 residues within 4Å: Chain A: P.270, N.274, F.518, S.539 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.539, A:S.539, A:S.539 NAG-NAG.2: 6 residues within 4Å: Chain A: I.34, D.35, Y.72, N.74, H.78, K.81 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.124, L.221, N.223, T.225, I.227 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.227 NAG-NAG.4: 6 residues within 4Å: Chain B: I.34, D.35, Y.72, N.74, H.78, K.81 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: P.270, N.274, F.518, S.539 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.539 NAG-NAG.7: 4 residues within 4Å: Chain C: P.270, N.274, F.518, S.539 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain D: P.270, N.274, F.518, S.539 3 PLIP interactions: 3 interactions with chain D Water bridges: D:S.539, D:S.539, D:S.539 NAG-NAG.30: 6 residues within 4Å: Chain D: I.34, D.35, Y.72, N.74, H.78, K.81 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain D: N.124, L.221, N.223, T.225, I.227 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.227 NAG-NAG.32: 6 residues within 4Å: Chain E: I.34, D.35, Y.72, N.74, H.78, K.81 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain E: P.270, N.274, F.518, S.539 1 PLIP interactions: 1 interactions with chain E Water bridges: E:S.539 NAG-NAG.35: 4 residues within 4Å: Chain F: P.270, N.274, F.518, S.539 No protein-ligand interaction detected (PLIP)

4 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC-NAG.6: 4 residues within 4Å: Chain B: N.124, L.221, N.223, T.225 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.8: 2 residues within 4Å: Chain C: P.505, N.507 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.34: 4 residues within 4Å: Chain E: N.124, L.221, N.223, T.225 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.36: 2 residues within 4Å: Chain F: P.505, N.507 No protein-ligand interaction detected (PLIP)

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

FE.9: 6 residues within 4Å: Chain A: D.253, D.294, Y.297, H.460 Ligands: MN.10, PO4.14 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.253, A:D.294, A:Y.297, A:H.460 FE.17: 6 residues within 4Å: Chain B: D.253, D.294, Y.297, H.460 Ligands: MN.18, PO4.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.253, B:D.294, B:Y.297, B:H.460 FE.22: 6 residues within 4Å: Chain C: D.253, D.294, Y.297, H.460 Ligands: MN.23, PO4.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.253, C:D.294, C:Y.297, C:H.460 FE.37: 6 residues within 4Å: Chain D: D.253, D.294, Y.297, H.460 Ligands: MN.38, PO4.42 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.253, D:D.294, D:Y.297, D:H.460 FE.45: 6 residues within 4Å: Chain E: D.253, D.294, Y.297, H.460 Ligands: MN.46, PO4.49 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.253, E:D.294, E:Y.297, E:H.460 FE.50: 6 residues within 4Å: Chain F: D.253, D.294, Y.297, H.460 Ligands: MN.51, PO4.55 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.253, F:D.294, F:Y.297, F:H.460

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.10: 7 residues within 4Å: Chain A: D.253, D.294, N.327, H.416, H.458 Ligands: FE.9, PO4.14 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.294, A:H.416, A:H.458 MN.18: 7 residues within 4Å: Chain B: D.253, D.294, N.327, H.416, H.458 Ligands: FE.17, PO4.21 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.294, B:H.416, B:H.458 MN.23: 7 residues within 4Å: Chain C: D.253, D.294, N.327, H.416, H.458 Ligands: FE.22, PO4.27 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.294, C:H.416, C:H.458 MN.38: 7 residues within 4Å: Chain D: D.253, D.294, N.327, H.416, H.458 Ligands: FE.37, PO4.42 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.294, D:H.416, D:H.458 MN.46: 7 residues within 4Å: Chain E: D.253, D.294, N.327, H.416, H.458 Ligands: FE.45, PO4.49 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.294, E:H.416, E:H.458 MN.51: 7 residues within 4Å: Chain F: D.253, D.294, N.327, H.416, H.458 Ligands: FE.50, PO4.55 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.294, F:H.416, F:H.458

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain A: R.247, K.522, T.524, R.536 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.522, A:T.524, A:R.536, A:R.536 Water bridges: A:R.247, A:D.285, A:D.285 GOL.15: 4 residues within 4Å: Chain A: N.30, P.32, D.82, T.83 No protein-ligand interaction detected (PLIP) GOL.16: 3 residues within 4Å: Chain A: Q.542, V.543, Y.544 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.540, A:V.543, A:V.543 GOL.28: 6 residues within 4Å: Chain B: E.361 Chain C: S.369, R.376, K.398, C.399, S.402 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.369, C:K.398, C:S.402, B:E.361 Water bridges: C:S.369, C:D.371 GOL.39: 4 residues within 4Å: Chain D: R.247, K.522, T.524, R.536 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.522, D:T.524, D:T.524, D:R.536, D:R.536 Water bridges: D:R.247, D:D.285, D:D.285 GOL.43: 4 residues within 4Å: Chain D: N.30, P.32, D.82, T.83 No protein-ligand interaction detected (PLIP) GOL.44: 3 residues within 4Å: Chain D: Q.542, V.543, Y.544 2 PLIP interactions: 2 interactions with chain D Water bridges: D:V.543, D:V.543 GOL.56: 6 residues within 4Å: Chain E: E.361 Chain F: S.369, R.376, K.398, C.399, S.402 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:S.369, F:K.398, F:S.402, E:E.361 Water bridges: F:S.369, F:D.371

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

NAG.12: 4 residues within 4Å: Chain A: T.474, N.475, N.484, N.486 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.484, A:N.486 Water bridges: A:V.561 NAG.13: 2 residues within 4Å: Chain A: P.505, N.507 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.507 Water bridges: A:K.514 NAG.19: 3 residues within 4Å: Chain B: N.484, N.486, V.561 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.486 Water bridges: B:V.561 NAG.20: 2 residues within 4Å: Chain B: P.505, N.507 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.507 NAG.24: 2 residues within 4Å: Chain C: I.34, N.74 No protein-ligand interaction detected (PLIP) NAG.25: 3 residues within 4Å: Chain C: L.221, N.223, T.225 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.225, C:T.225 NAG.26: 2 residues within 4Å: Chain C: N.484, N.486 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.484, C:N.484, C:C.559 NAG.40: 4 residues within 4Å: Chain D: T.474, N.475, N.484, N.486 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.484, D:N.486 Water bridges: D:V.561 NAG.41: 2 residues within 4Å: Chain D: P.505, N.507 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.507 Water bridges: D:K.514 NAG.47: 3 residues within 4Å: Chain E: N.484, N.486, V.561 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.486 Water bridges: E:N.484, E:V.561 NAG.48: 2 residues within 4Å: Chain E: P.505, N.507 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.507 NAG.52: 2 residues within 4Å: Chain F: I.34, N.74 No protein-ligand interaction detected (PLIP) NAG.53: 3 residues within 4Å: Chain F: L.221, N.223, T.225 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.225, F:T.225 NAG.54: 2 residues within 4Å: Chain F: N.484, N.486 3 PLIP interactions: 3 interactions with chain F Water bridges: F:N.484, F:N.484, F:C.559

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

PO4.14: 9 residues within 4Å: Chain A: D.253, D.294, Y.297, N.327, H.328, H.458, H.460 Ligands: FE.9, MN.10 6 PLIP interactions: 6 interactions with chain A Water bridges: A:H.458, A:H.460, A:H.460 Salt bridges: A:H.328, A:H.458, A:H.460 PO4.21: 9 residues within 4Å: Chain B: D.253, D.294, Y.297, N.327, H.328, H.458, H.460 Ligands: FE.17, MN.18 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.328, B:H.458, B:H.460 PO4.27: 9 residues within 4Å: Chain C: D.253, D.294, Y.297, N.327, H.328, H.458, H.460 Ligands: FE.22, MN.23 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.253, C:D.294, C:D.294, C:N.327 Salt bridges: C:H.328, C:H.458, C:H.460 PO4.42: 9 residues within 4Å: Chain D: D.253, D.294, Y.297, N.327, H.328, H.458, H.460 Ligands: FE.37, MN.38 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.327 Water bridges: D:H.458, D:H.460, D:H.460 Salt bridges: D:H.328, D:H.458, D:H.460 PO4.49: 9 residues within 4Å: Chain E: D.253, D.294, Y.297, N.327, H.328, H.458, H.460 Ligands: FE.45, MN.46 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.253, E:D.294, E:N.327 Water bridges: E:H.458, E:H.460 Salt bridges: E:H.328, E:H.458, E:H.460 PO4.55: 9 residues within 4Å: Chain F: D.253, D.294, Y.297, N.327, H.328, H.458, H.460 Ligands: FE.50, MN.51 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.327 Salt bridges: F:H.328, F:H.458, F:H.460

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antonyuk, S.V. et al., The Structure of a Purple Acid Phosphatase Involved in Plant Growth and Pathogen Defence Exhibits a Novel Immunoglobulin-Like Fold. Iucrj (2014)

Release Date

2014-01-29

Peptides

DIPHOSPHONUCLEOTIDE PHOSPHATASE 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

DIPHOSPHONUCLEOTIDE PHOSPHATASE 1