2O86
Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2O86/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Bubalus bubalis
- Mutation(s): No 
- Deposited: 2006-12-12 Released: 2006-12-26 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.218 
- R-Value Work: 0.209 
- R-Value Observed: 0.209 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
Lactoperoxidase | 595 | Bubalus bubalis | Mutation(s): 0  EC: 1.11.1.7 | ||
UniProt | |||||
Find proteins for A5JUY8 (Bubalus bubalis) Explore A5JUY8  Go to UniProtKB:  A5JUY8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A5JUY8 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HEM Query on HEM | V [auth A] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
IOD Query on IOD | H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M | |||
NO3 Query on NO3 | O [auth A] P [auth A] Q [auth A] R [auth A] S [auth A] | NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N | |||
CO3 Query on CO3 | G [auth A] | CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L | |||
CA Query on CA | F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.218 
- R-Value Work: 0.209 
- R-Value Observed: 0.209 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 54.535 | α = 90 |
b = 80.833 | β = 102.96 |
c = 77.655 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MAR345 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
Entry History 
Deposition Data
- Released Date: 2006-12-26  Deposition Author(s): Sheikh, I.A., Singh, N., Singh, A.K., Sharma, S., Kaur, P., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2006-12-26
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary