SMTL ID : 1xzw.1

Sweet potato purple acid phosphatase/phosphate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-MAN-FUC.1: 2 residues within 4Å: Chain A: N.80, N.172 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-FUC.6: 4 residues within 4Å: Chain B: K.394, N.395, H.398, W.418 No protein-ligand interaction detected (PLIP)

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.2: 7 residues within 4Å: Chain A: M.9, S.13, D.14, H.139, N.142, T.146, R.187 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.3: 4 residues within 4Å: Chain A: K.394, N.395, H.398, W.418 No protein-ligand interaction detected (PLIP) NAG-FUC.4: 1 residues within 4Å: Chain A: N.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.273

2 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

NAG-FUC-NAG.5: 4 residues within 4Å: Chain B: Y.79, N.80, P.171, N.172 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.176 Hydrophobic interactions: B:P.171 NAG-FUC-NAG.7: 3 residues within 4Å: Chain B: N.273, S.275, E.276 No protein-ligand interaction detected (PLIP)

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

FE.8: 8 residues within 4Å: Chain A: D.134, D.163, Y.166, H.201, H.322, H.324 Ligands: MN.9, PO4.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.134, A:D.163, A:Y.166, A:H.324 FE.13: 8 residues within 4Å: Chain B: D.134, D.163, Y.166, H.201, H.322, H.324 Ligands: MN.14, PO4.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.134, B:D.163, B:Y.166, B:H.324

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

MN.9: 7 residues within 4Å: Chain A: D.134, D.163, N.200, H.285, H.322 Ligands: FE.8, PO4.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.163, A:H.285, A:H.322 MN.14: 7 residues within 4Å: Chain B: D.134, D.163, N.200, H.285, H.322 Ligands: FE.13, PO4.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.163, B:H.285, B:H.322

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

PO4.10: 11 residues within 4Å: Chain A: D.134, D.163, Y.166, N.200, H.201, H.295, H.322, H.324, E.365 Ligands: FE.8, MN.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.200, A:E.365 Salt bridges: A:H.201, A:H.295, A:H.322, A:H.324 PO4.11: 5 residues within 4Å: Chain A: R.331, W.418, L.419, L.420, R.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.418, A:L.420 Salt bridges: A:R.331, A:R.422 PO4.15: 10 residues within 4Å: Chain B: D.163, Y.166, N.200, H.201, H.295, H.322, H.324, E.365 Ligands: FE.13, MN.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.365 Salt bridges: B:H.201, B:H.295, B:H.322, B:H.324 PO4.16: 5 residues within 4Å: Chain B: R.331, W.418, L.419, L.420, R.422 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.420 Salt bridges: B:R.331, B:R.422

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

NAG.12: 5 residues within 4Å: Chain B: D.14, H.139, N.142, T.146, R.187 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.14, B:D.14, B:D.14, B:H.139, B:N.142, B:T.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schenk, G. et al., Phosphate forms an unusual tripodal complex with the Fe-Mn center of sweet potato purple acid phosphatase. Proc.Natl.Acad.Sci.USA (2005)

Release Date

2004-12-14

Peptides

purple acid phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

purple acid phosphatase