4P8W
The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc4) were solved to resolutions of 1.9 angstrom
- PDB DOI: https://doi.org/10.2210/pdb4P8W/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2014-04-01 Released: 2014-12-03
- Funding Organization(s): The Higher Education Commission
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.236
- R-Value Work: 0.186
- R-Value Observed: 0.188
wwPDB Validation 3D Report Full Report
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 |
| Chitinase-3-like protein 2 | 371 | Homo sapiens | Mutation(s): 2 Gene Names: CHI3L2 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q15782 (Homo sapiens) Explore Q15782 Go to UniProtKB: Q15782 | |||||
PHAROS: Q15782 GTEx: ENSG00000064886 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q15782 | ||||
Sequence AnnotationsExpand | |||||
| |||||
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose | B | 4 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G93613RO GlyCosmos: G93613RO GlyGen: G93613RO | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A], D [auth A], E [auth A], F [auth A], G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.236
- R-Value Work: 0.186
- R-Value Observed: 0.188
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 71.354 | α = 90 |
| b = 71.354 | β = 90 |
| c = 140.528 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2014-12-03 Deposition Author(s): Suginta, W., Ranok, A., Robinson, R.C., Wongsantichon, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| The Higher Education Commission | Thailand | CHE500307 |
Revision History (Full details and data files)
- Version 1.0: 2014-12-03
Type: Initial release - Version 1.1: 2014-12-17
Changes: Database references - Version 1.2: 2015-02-04
Changes: Derived calculations - Version 1.3: 2015-02-11
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary - Version 2.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary
