3ERH
First structural evidence of substrate specificity in mammalian peroxidases: Crystal structures of substrate complexes with lactoperoxidases from two different species
- PDB DOI: https://doi.org/10.2210/pdb3ERH/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Bubalus bubalis
- Mutation(s): No 
- Deposited: 2008-10-02 Released: 2009-03-31 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.195 
- R-Value Work: 0.180 
- R-Value Observed: 0.180 
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
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B, C | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G08918EL GlyCosmos:  G08918EL GlyGen:  G08918EL |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HEM Query on HEM | F [auth A] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
IOD Query on IOD | J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M | |||
SCN Query on SCN | G [auth A], H [auth A] | THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M | |||
CA Query on CA | I [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: 2.40 Å
- R-Value Free: 0.195 
- R-Value Work: 0.180 
- R-Value Observed: 0.180 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 54.207 | α = 90 |
b = 80.541 | β = 102.64 |
c = 77.877 | γ = 90 |
Software Name | Purpose |
---|---|
MAR345dtb | data collection |
AMoRE | phasing |
CNS | refinement |
AUTOMAR | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-03-31  Deposition Author(s): Sheikh, I.A., Singh, N., Singh, A.K., Sinha, M., Singh, S.B., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2009-03-31
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary