6BMT
Crystal Structure of a Recombinant form of Human Myeloperoxidase Bound to an Inhibitor from Staphylococcus delphini
- PDB DOI: https://doi.org/10.2210/pdb6BMT/pdb
- Classification: OXIDOREDUCTASE/INHIBITOR
- Organism(s): Homo sapiens, Staphylococcus delphini
- Expression System: Mus musculus, Escherichia coli
- Mutation(s): No
- Deposited: 2017-11-15 Released: 2018-01-03
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.218
- R-Value Work: 0.185
- R-Value Observed: 0.187
This is version 1.5 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 |
| Myeloperoxidase | 745 | Homo sapiens | Mutation(s): 0 Gene Names: MPO EC: 1.11.2.2 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P05164 (Homo sapiens) Explore P05164 Go to UniProtKB: P05164 | |||||
PHAROS: P05164 GTEx: ENSG00000005381 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P05164 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Hypothetical Protein | 105 | Staphylococcus delphini | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A0A2A4GXB5 (Staphylococcus delphini) Explore A0A2A4GXB5 Go to UniProtKB: A0A2A4GXB5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2A4GXB5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEM Query on HEM | D [auth A] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | ||
| NAG Query on NAG | F [auth A], G [auth A], H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.218
- R-Value Work: 0.185
- R-Value Observed: 0.187
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 84.626 | α = 90 |
| b = 90.674 | β = 90 |
| c = 125.661 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-01-03 Deposition Author(s): Ploscariu, N.T., Geisbrecht, B.V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM121511 |
Revision History (Full details and data files)
- Version 1.0: 2018-01-03
Type: Initial release - Version 1.1: 2018-03-21
Changes: Database references - Version 1.2: 2018-03-28
Changes: Data collection, Database references - Version 1.3: 2020-01-01
Changes: Author supporting evidence - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
