10JV | pdb_000010jv

Crystal structure of human CHI3L1 in complex with the CHI-DEL small molecule

PDB DOI: https://doi.org/10.2210/pdb10JV/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2026-01-22 Released: 2026-08-05
Deposition Author(s): Upadhyay, S., Zhang, L., Teplova, M., Gabr, M.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.253 (Depositor), 0.255 (DCC)
R-Value Work:
0.215 (Depositor), 0.217 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 10JV

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human CHI3L1 in complex with the CHI-DEL small molecule

Upadhyay, S., Zhang, L., Teplova, M., Gabr, M.

To be published.

Macromolecule Content

Total Structure Weight: 183.19 kDa
Atom Count: 11,664
Modeled Residue Count: 1,442
Deposited Residue Count: 1,604
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-3-like protein 1	A, B, C, D	401	Homo sapiens	Mutation(s): 1 Gene Names: CHI3L1
UniProt & NIH Common Fund Data Resources
Find proteins for P36222 (Homo sapiens) Explore P36222 Go to UniProtKB: P36222
PHAROS: P36222 GTEx: ENSG00000133048
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36222
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P36222-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C9M( Subject of Investigation/LOI) Query on A1C9M Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D]	J [auth A], K [auth B], L [auth C], M [auth D]	(4S)-4-(4-fluoronaphthalene-1-sulfonamido)-N-methyl-1-(2-methyl-1,3-benzoxazole-6-carbonyl)-L-prolinamide C₂₅ H₂₃ F N₄ O₅ S MDVBZODLICLQSO-KKSFZXQISA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.253 (Depositor), 0.255 (DCC)
R-Value Work: 0.215 (Depositor), 0.217 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.956	α = 90
b = 122.309	β = 90
c = 136.304	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS136524

Revision History (Full details and data files)

Version 1.0: 2026-08-05
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.