SMTL ID : 7dlh.1

Crystallization of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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(Non-covalent)

NAG-NAG.1: 5 residues within 4Å: Chain A: D.94, N.331, S.333, A.334 Ligands: FUC.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.94

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

NAG-MAN-NAG.2: 5 residues within 4Å: Chain A: N.233, R.258, N.273, R.274, E.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.273

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 25 residues within 4Å: Chain A: A.72, G.73, L.75, R.76, F.79, P.107, N.108, R.112, P.180, P.181, P.182, L.206, G.209, H.210, I.212, G.213, L.214, G.215, H.216, S.219, R.252, L.255, F.278, S.280, M.312 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:A.72, A:L.75, A:R.76, A:F.79, A:F.79, A:N.108, A:P.182, A:L.206, A:L.255, A:F.278 Hydrogen bonds: A:L.214, A:H.216, A:S.219, A:S.219 Water bridges: A:R.76, A:R.76, A:R.76, A:R.76 Salt bridges: A:R.112, A:R.252 pi-Stacking: A:F.79 Metal complexes: A:H.210, H2O.5

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.4: 2 residues within 4Å: Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: T.211, D.256, T.259, I.262, D.264 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.211, A:T.211, A:D.256, A:T.259, A:I.262

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain A: D.81, V.84, G.86, D.88, S.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.86, A:D.88, A:D.88, A:S.90

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: S.330, N.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.330, A:N.336 Water bridges: A:S.133, A:N.336

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: D.124, R.125, R.128 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: H.216, G.248, D.250 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: Q.301, F.305 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, x.d. et al., Crystallization of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites. To Be Published

Release Date

2021-12-01

Peptides

peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

peroxidase