8qkb

Crystal structure of human cathepsin L in complex with the vinyl sulfone inhibitor K777

Method: X-RAY DIFFRACTION

▼

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

Cathepsin L

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-{(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}-L-PHENYLALANINAMIDE × 4 TETRAETHYLENE GLYCOL × 1 1,2-ETHANEDIOL × 12 DI(HYDROXYETHYL)ETHER × 5 DIMETHYL SULFOXIDE × 6 TRIETHYLENE GLYCOL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CATL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 114–333 Author chain B； PDBConstruct 1–220； UniProt 114–333 Author chain C； PDBConstruct 1–220； UniProt 114–333 Author chain D； PDBConstruct 1–220； UniProt 114–333

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8qkb
Deposition date deposition_date	2023-09-14
Structure title title	Crystal structure of human cathepsin L in complex with the vinyl sulfone inhibitor K777
Keywords keywords	cystein protease, drug target, lysosome, virus cell entry, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8qkb__assembly_1__model_1

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

Download this curve (.dat)

8qkb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qkb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.99 Å
Rg (electron density)	29.05 Å
Total Rg	29.83 Å
Atom count	7264
Residues	876
Excluded volume	124360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qkb__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Cathepsin L
Molecular weight formula_weight	24161.7 kDa
Mutation mutation	T110A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8065

APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDAGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Komagataella phaffii GS115

Entity 2 Entity 2 non-polymer

Description description	NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-{(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}-L-PHENYLALANINAMIDE
Molecular weight formula_weight	576.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	686

▶

Unit-cell length a length_a	56.990 Å
Unit-cell length b length_b	62.440 Å
Unit-cell length c length_c	67.750 Å
Unit-cell angle α angle_alpha	105.41 °
Unit-cell angle β angle_beta	93.65 °
Unit-cell angle γ angle_gamma	115.53 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	44.190 Å
R factor r_factor	0.1576
R_work r_work	0.1572
R_free r_free	0.1867

Crystal structure of human cathepsin L in complex with the vinyl sulfone inhibitor K777

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

Cathepsin L

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

8qkb__assembly_1__model_1

8qkb__assembly_1__model_1 | I(q)

8qkb__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of human cathepsin L in complex with the vinyl sulfone inhibitor K777

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

Cathepsin L

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

8qkb__assembly_1__model_1

8qkb__assembly_1__model_1 | I(q)

8qkb__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)