SAXSdb — 4l19

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

Collagenase 3

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	ZINC ION × 3 CALCIUM ION × 2 FORMIC ACID × 1 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one × 2 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 2 FORMIC ACID × 4 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one × 1 GLYCEROL × 2 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 10 CALCIUM ION × 8 FORMIC ACID × 10 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one × 6 GLYCEROL × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MMP13_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 104–274 Author chain B； PDBConstruct 1–171； UniProt 104–274

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	4l19
Deposition date deposition_date	2013-06-02
Structure title title	Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1
Keywords keywords	metalloprotease, hydrolase, MMP-13, collagenase, exosite inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

4l19__assembly_1__model_1

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

Download this curve (.dat)

4l19__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4l19__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.59 Å
Rg (electron density)	15.44 Å
Total Rg	16.71 Å
Atom count	1373
Residues	166
Excluded volume	24447 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4l19__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4l19__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4l19__assembly_3__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	Collagenase 3
Molecular weight formula_weight	19235.4 kDa
EC 编号 ec_number	3.4.24.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3061

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one
Molecular weight formula_weight	272.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	268

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4l19a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

Domain ID domain_id	d4l19b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	4l19A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4l19B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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Unit-cell length a length_a	135.320 Å
Unit-cell length b length_b	36.029 Å
Unit-cell length c length_c	95.814 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	130.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.660 Å
Low-resolution limit resolution_low	47.750 Å
R factor r_factor	0.1370
R_work r_work	0.1340
R_free r_free	0.1990

Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1

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

Collagenase 3

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

4l19__assembly_1__model_1

4l19__assembly_1__model_1 | I(q)

4l19__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1

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

Collagenase 3

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

4l19__assembly_1__model_1

4l19__assembly_1__model_1 | I(q)

4l19__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)