6ERC
Peroxidase A from Dictyostelium discoideum (DdPoxA)
- PDB DOI: https://doi.org/10.2210/pdb6ERC/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Dictyostelium discoideum
- Expression System: Komagataella pastoris
- Mutation(s): No 
- Deposited: 2017-10-17 Released: 2017-12-27 
- Funding Organization(s): Austrian Science Fund
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.257 
- R-Value Work: 0.228 
- R-Value Observed: 0.229 
wwPDB Validation   3D Report Full Report
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Peroxinectin A | 511 | Dictyostelium discoideum | Mutation(s): 0  Gene Names: poxA, DDB_G0277275 EC: 1.11.1.7 | ||
UniProt | |||||
Find proteins for Q6TMK4 (Dictyostelium discoideum) Explore Q6TMK4  Go to UniProtKB:  Q6TMK4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6TMK4 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 8 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HEM (Subject of Investigation/LOI) Query on HEM | F [auth A], M [auth B] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
NAG Query on NAG | C [auth A], D [auth A], E [auth A], N [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
BMA Query on BMA | H [auth A] | beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N | |||
MRD Query on MRD | O [auth B] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N | |||
MPD Query on MPD | I [auth A], P [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N | |||
CA Query on CA | G [auth A], L [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | J [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | K [auth A], Q [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.257 
- R-Value Work: 0.228 
- R-Value Observed: 0.229 
- Space Group: P 31 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 128.253 | α = 90 |
b = 128.253 | β = 90 |
c = 146.015 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
BALBES | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-12-27  Deposition Author(s): Nicolussi, A., Mlynek, G., Furtmueller, P.G., Djinovic-Carugo, K., Obinger, C.
Funding Organization | Location | Grant Number |
---|---|---|
Austrian Science Fund | Austria | W1224 |
Revision History (Full details and data files)
- Version 1.0: 2017-12-27
Type: Initial release - Version 1.1: 2018-01-31
Changes: Author supporting evidence - Version 1.2: 2018-02-07
Changes: Database references, Source and taxonomy - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary