6ze8

Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound OATD-01

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chitotriosidase-1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine × 1 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine × 1 SODIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine × 1 SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine × 1 SODIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine × 1 SODIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine × 1 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHIT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–365； UniProt 22–386 Author chain B； PDBConstruct 1–365； UniProt 22–386 Author chain C； PDBConstruct 1–365； UniProt 22–386 Author chain D； PDBConstruct 1–365； UniProt 22–386 Author chain E； PDBConstruct 1–365； UniProt 22–386 Author chain F； PDBConstruct 1–365； UniProt 22–386

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ze8
Deposition date deposition_date	2020-06-16
Structure title title	Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound OATD-01
Keywords keywords	chitinase, chitin binding, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6ze8__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6ze8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ze8__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.27 Å
Rg (electron density)	19.88 Å
Total Rg	20.81 Å
Atom count	2854
Residues	365
Excluded volume	50490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ze8__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ze8__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6ze8__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6ze8__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6ze8__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6ze8__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Chitotriosidase-1
Molecular weight formula_weight	40784.7 kDa
EC 编号 ec_number	3.2.1.14
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	20052

AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine
Molecular weight formula_weight	390.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2370

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6ze8a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d6ze8a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

Domain ID domain_id	d6ze8b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d6ze8b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

Domain ID domain_id	d6ze8c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d6ze8c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

Domain ID domain_id	d6ze8d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d6ze8d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

Domain ID domain_id	d6ze8e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d6ze8e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

Domain ID domain_id	d6ze8f1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d6ze8f2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

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Unit-cell length a length_a	87.325 Å
Unit-cell length b length_b	93.744 Å
Unit-cell length c length_c	281.642 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	47.340 Å
R factor r_factor	0.1232
R_work r_work	0.1227
R_free r_free	0.1679

Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound OATD-01

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chitotriosidase-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ze8__assembly_1__model_1

6ze8__assembly_1__model_1 | I(q)

6ze8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (1)

Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound OATD-01

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chitotriosidase-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ze8__assembly_1__model_1

6ze8__assembly_1__model_1 | I(q)

6ze8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (1)