5GLS
Structure of bovine Lactoperoxidase with a partially modified covalent bond with heme moiety
- PDB DOI: https://doi.org/10.2210/pdb5GLS/pdb
- Entry: 5GLS supersedes: 4S0Y
- Classification: OXIDOREDUCTASE
- Organism(s): Bos taurus
- Mutation(s): No 
- Deposited: 2016-07-12 Released: 2016-07-27 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.93 Å
- R-Value Free: 0.245 
- R-Value Work: 0.192 
- R-Value Observed: 0.195 
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 | Bos taurus | Mutation(s): 0  EC: 1.11.1.7 | ||
UniProt | |||||
Find proteins for P80025 (Bos taurus) Explore P80025  Go to UniProtKB:  P80025 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80025 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HEM Query on HEM | G [auth A] | 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] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
IOD Query on IOD | I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M | |||
GOL Query on GOL | CA [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
OSM Query on OSM | AA [auth A], BA [auth A] | 1-(OXIDOSULFANYL)METHANAMINE C H5 N O S KONFWJXIYYGXOO-UHFFFAOYSA-N | |||
SCN Query on SCN | H [auth A] | THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M | |||
CA Query on CA | F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
SEP Query on SEP | A | L-PEPTIDE LINKING | C3 H8 N O6 P | SER |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.93 Å
- R-Value Free: 0.245 
- R-Value Work: 0.192 
- R-Value Observed: 0.195 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 54.005 | α = 90 |
b = 79.834 | β = 102.3 |
c = 76.126 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2016-07-27  Deposition Author(s): Tiwari, P., Singh, P.K., Sirohi, H.V., Kaur, P., Sharma, S., Singh, T.P.
- This entry supersedes: 4S0Y
Revision History (Full details and data files)
- Version 1.0: 2016-07-27
Type: Initial release - Version 1.1: 2017-02-01
Changes: Database references - Version 1.2: 2018-07-18
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary