4CYF
The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
- PDB DOI: https://doi.org/10.2210/pdb4CYF/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes
- Deposited: 2014-04-11 Released: 2014-12-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.222
- R-Value Work: 0.195
- R-Value Observed: 0.197
This is version 3.0 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 |
| PANTETHEINASE | 506 | Homo sapiens | Mutation(s): 1 EC: 3.5.1.92 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O95497 (Homo sapiens) Explore O95497 Go to UniProtKB: O95497 | |||||
PHAROS: O95497 GTEx: ENSG00000112299 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O95497 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth A] E [auth A] F [auth A] G [auth B] H [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSO Query on CSO | A, B | L-PEPTIDE LINKING | C3 H7 N O3 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.222
- R-Value Work: 0.195
- R-Value Observed: 0.197
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 119.941 | α = 90 |
| b = 119.941 | β = 90 |
| c = 221.887 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| Auto-Rickshaw | phasing |
Entry History
Deposition Data
- Released Date: 2014-12-10 Deposition Author(s): Boersma, Y.L., Newman, J., Adams, T.E., Sparrow, L., Cowieson, N., Lucent, D., Krippner, G., Bozaoglu, K., Peat, T.S.
Revision History (Full details and data files)
- Version 1.0: 2014-12-10
Type: Initial release - Version 1.1: 2015-02-25
Changes: Database references - Version 2.0: 2017-06-14
Changes: Advisory, Atomic model, Derived calculations - Version 2.1: 2019-05-08
Changes: Data collection, Experimental preparation - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
