4AY1
Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide binding properties
- PDB DOI: https://doi.org/10.2210/pdb4AY1/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Komagataella phaffii GS115
- Mutation(s): No 
- Deposited: 2012-06-17 Released: 2012-08-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.239 
- R-Value Work: 0.191 
- R-Value Observed: 0.192 
wwPDB Validation   3D Report Full Report
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 |
CHITINASE-3-LIKE PROTEIN 2 | 365 | Homo sapiens | Mutation(s): 0  | ||
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 | |||||
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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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X | 4 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G01361SX GlyCosmos:  G01361SX GlyGen:  G01361SX |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.239 
- R-Value Work: 0.191 
- R-Value Observed: 0.192 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 255.686 | α = 90 |
b = 152.543 | β = 94.62 |
c = 138.186 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
Entry History 
Deposition Data
- Released Date: 2012-08-08  Deposition Author(s): Schimpl, M., Rush, C.L., Betou, M., Eggleston, I.M., Penman, G.A., Recklies, A.D., van Aalten, D.M.F.
Revision History (Full details and data files)
- Version 1.0: 2012-08-08
Type: Initial release - Version 2.0: 2018-04-11
Changes: Advisory, Atomic model, Data collection, Derived calculations - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary