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- PDB-10jv: Crystal structure of human CHI3L1 in complex with the CHI-DEL sma... -

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Basic information

Entry
Database: PDB / ID: 10jv
TitleCrystal structure of human CHI3L1 in complex with the CHI-DEL small molecule
ComponentsChitinase-3-like protein 1
KeywordsHYDROLASE / CHI3L1 / Glycosyl hydrolase 18 / Glioblastoma / CHI-DEL complex / Del Screening
Function / homology
Function and homology information


transforming growth factor beta1 production / response to interleukin-6 / cartilage development / chitin catabolic process / chitin binding / extracellular matrix structural constituent / lung development / ERK1 and ERK2 cascade / response to tumor necrosis factor / response to mechanical stimulus ...transforming growth factor beta1 production / response to interleukin-6 / cartilage development / chitin catabolic process / chitin binding / extracellular matrix structural constituent / lung development / ERK1 and ERK2 cascade / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of interleukin-8 production / cellular response to tumor necrosis factor / specific granule lumen / positive regulation of angiogenesis / carbohydrate binding / extracellular matrix / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / : / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
: / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Chitinase-3-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsUpadhyay, S. / Zhang, L. / Teplova, M. / Gabr, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS136524 United States
CitationJournal: To Be Published
Title: Crystal structure of human CHI3L1 in complex with the CHI-DEL small molecule
Authors: Upadhyay, S. / Zhang, L. / Teplova, M. / Gabr, M.
History
DepositionJan 22, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase-3-like protein 1
B: Chitinase-3-like protein 1
C: Chitinase-3-like protein 1
D: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,19113
Polymers179,3594
Non-polymers3,8329
Water1,35175
1
A: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8674
Polymers44,8401
Non-polymers1,0273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7753
Polymers44,8401
Non-polymers9352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7753
Polymers44,8401
Non-polymers9352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7753
Polymers44,8401
Non-polymers9352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.956, 122.309, 136.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chitinase-3-like protein 1 / 39 kDa synovial protein / Cartilage glycoprotein 39 / CGP-39 / GP-39 / hCGP-39 / YKL-40


Mass: 44839.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P36222
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-A1C9M / (4S)-4-(4-fluoronaphthalene-1-sulfonamido)-N-methyl-1-(2-methyl-1,3-benzoxazole-6-carbonyl)-L-prolinamide


Mass: 510.537 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C25H23FN4O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium nitrate, 20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.81→34.58 Å / Num. obs: 45095 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.948 / Rmerge(I) obs: 0.262 / Rpim(I) all: 0.134 / Rrim(I) all: 0.296 / Χ2: 1 / Net I/σ(I): 5.9 / Num. measured all: 253361
Reflection shellResolution: 2.81→2.96 Å / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.196 / Num. measured all: 38083 / Num. unique obs: 6515 / CC1/2: 0.418 / Rpim(I) all: 0.626 / Rrim(I) all: 1.356 / Χ2: 0.94 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→34.58 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1997 4.46 %
Rwork0.2151 --
obs0.2168 44815 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11331 0 262 75 11668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311906
X-RAY DIFFRACTIONf_angle_d0.67916163
X-RAY DIFFRACTIONf_dihedral_angle_d17.0334350
X-RAY DIFFRACTIONf_chiral_restr0.041727
X-RAY DIFFRACTIONf_plane_restr0.0112052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.34061400.29322976X-RAY DIFFRACTION98
2.88-2.960.27781400.28763004X-RAY DIFFRACTION99
2.96-3.040.31531400.29073000X-RAY DIFFRACTION100
3.04-3.140.3641410.28033037X-RAY DIFFRACTION100
3.14-3.250.31891410.26513016X-RAY DIFFRACTION100
3.25-3.380.34641430.25313063X-RAY DIFFRACTION100
3.38-3.540.30921420.24823023X-RAY DIFFRACTION100
3.54-3.720.20671420.21363071X-RAY DIFFRACTION100
3.72-3.960.23551420.1883051X-RAY DIFFRACTION100
3.96-4.260.18971440.18413071X-RAY DIFFRACTION100
4.26-4.690.20661440.16763061X-RAY DIFFRACTION100
4.69-5.370.19441420.16353080X-RAY DIFFRACTION99
5.37-6.750.25261450.20743132X-RAY DIFFRACTION100
6.75-34.580.2241510.18713233X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.11350.2456-0.40961.921-0.13060.664-0.0192-0.05560.2260.02240.0292-0.1363-0.0978-0.0118-0.01310.2464-0.0033-0.02470.1470.00010.2577-23.968922.6853-32.2197
22.6708-0.33290.3222.1993-0.1310.5071-0.02140.2148-0.2148-0.0744-0.0124-0.20180.08550.01560.03510.2494-0.00080.03250.1645-0.03680.1906-26.2336-23.273-35.7008
32.2040.34630.17941.63420.37081.94820.0995-0.19530.0030.3642-0.32980.57890.1516-0.56910.11120.3921-0.12820.17130.4004-0.13610.3779-55.853-2.1288-7.8621
42.8040.4016-1.1161.3295-0.922.2430.32520.40570.3977-0.08050.41150.6112-0.1773-1.0126-0.44170.42760.10570.01310.6870.32140.4902-56.93113.049-59.4224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 383)
2X-RAY DIFFRACTION2chain 'B' and (resid 22 through 383)
3X-RAY DIFFRACTION3chain 'C' and (resid 22 through 383)
4X-RAY DIFFRACTION4chain 'D' and (resid 22 through 383)

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