7DLH | pdb_00007dlh

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

PDB DOI: https://doi.org/10.2210/pdb7DLH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Panicum miliaceum
Expression System: Panicum miliaceum
Mutation(s): No

Deposited: 2020-11-27 Released: 2021-12-01
Deposition Author(s): Cui, x.d., Wang, t.f., Wang, k.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.205 (Depositor), 0.204 (DCC)
R-Value Work:
0.171 (Depositor), 0.173 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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

Cui, x.d., Wang, t.f.

To be published.

Macromolecule Content

Total Structure Weight: 38.35 kDa
Atom Count: 2,815
Modeled Residue Count: 302
Deposited Residue Count: 337
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peroxidase	A	337	Panicum miliaceum	Mutation(s): 0 EC: 1.11.1.7
UniProt
Find proteins for A0A3L6SKP5 (Panicum miliaceum) Explore A0A3L6SKP5 Go to UniProtKB: A0A3L6SKP5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3L6SKP5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2	N/A	N/A	Interactions Focus chain B Interactions & Density Focus chain B

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(2-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3	N/A	N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
FUC (Subject of Investigation/LOI) Query on FUC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]