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2PUM|pdb_00002pum
Crystal structure of bovine lactoperoxidase complex with catechol and iodide at 2.7 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2PUM/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Bos taurus
- Mutation(s): Yes
- Deposited: 2007-05-09 Released: 2007-05-22
- Deposition Author(s): Singh, A.K.,Singh, N.,Sharma, S.,Kaur, P.,Singh, T.P.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.203 (Depositor), 0.200 (DCC)
- R-Value Work: 0.165 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.167 (Depositor)
Starting Model:experimental
View more details
This is version 2.2 of the entry. See complete history.
Literature
Download MendeleyCrystal structure of bovine lactoperoxidase complex with catechol and iodide at 2.7 A resolution
Singh, A.K., Singh, N., Sharma, S., Kaur, P., Singh, T.P.To be published.
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (HEM)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 71.97 kDa
- Atom Count: 5,260
- Modelled Residue Count: 595
- Deposited Residue Count: 595
- Unique protein chains: 1
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lactoperoxidase | 595 | Bos taurus | Mutation(s): 1 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 | ||||
Glycosylation | |||||
| Glycosylation Sites: 4 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| 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 | B, D | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO | |||||
Small Molecules
| 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: 2.70 Å
- R-Value Free: 0.203 (Depositor), 0.200 (DCC)
- R-Value Work: 0.165 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.167 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.422 | α = 90 |
| b = 80.489 | β = 102.6 |
| c = 77.321 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MAR345dtb | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2007-05-22 Deposition Author(s): Singh, A.K.,Singh, N.,Sharma, S.,Kaur, P.,Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2007-05-22
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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.2: 2024-10-30
Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.