1hv5

CRYSTAL STRUCTURE OF THE STROMELYSIN-3 (MMP-11) CATALYTIC DOMAIN COMPLEXED WITH A PHOSPHINIC INHIBITOR

Method: X-RAY DIFFRACTION

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

STROMELYSIN 3

Mus musculus

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 × 2 CALCIUM ION × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 2 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MMP11_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 102–266 Author chain B； PDBConstruct 1–165； UniProt 102–266 Author chain C； PDBConstruct 1–165； UniProt 102–266 Author chain D； PDBConstruct 1–165； UniProt 102–266 Author chain E； PDBConstruct 1–165； UniProt 102–266 Author chain F； PDBConstruct 1–165； UniProt 102–266

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	1hv5
Deposition date deposition_date	2001-01-08
Structure title title	CRYSTAL STRUCTURE OF THE STROMELYSIN-3 (MMP-11) CATALYTIC DOMAIN COMPLEXED WITH A PHOSPHINIC INHIBITOR
Keywords keywords	stromelysin-3, inhibition, phosphinic inhibitor, 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.

1hv5__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1hv5__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1hv5__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	16.85 Å
Rg (electron density)	15.61 Å
Total Rg	16.74 Å
Atom count	1445
Residues	162
Excluded volume	25876 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1hv5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1hv5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1hv5__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1hv5__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1hv5__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1hv5__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 (6)

Entity 1 Entity 1 polymer

Description description	STROMELYSIN 3
Molecular weight formula_weight	19067.4 kDa
EC 编号 ec_number	3.4.24.-
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	10772

MFVLSGGRWEKTDLTYRILRFPWQLVREQVRQTVAEALQVWSEVTPLTFTEVHEGRADIMIDFARYWHGDNLPFDGPGGILAHAFFPKTHREGDVHFDYDETWTIGDNQGTDLLQVAAHEFGHVLGLQHTTAAKALMSPFYTFRYPLSLSPDDRRGIQHLYGRPQ

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21

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	12

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	6

Entity 4 Entity 4 non-polymer

Description description	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
Molecular weight formula_weight	614.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID
Molecular weight formula_weight	694.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2136

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1hv5a_
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	d1hv5b_
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	d1hv5c_
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	d1hv5d_
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	d1hv5e_
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	d1hv5f_
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 (6 domains)

Domain ID domain_id	1hv5A00
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	1hv5B00
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	1hv5C00
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	1hv5D00
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	1hv5E00
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	1hv5F00
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	140.100 Å
Unit-cell length b length_b	148.500 Å
Unit-cell length c length_c	91.400 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	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.890 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2620

CRYSTAL STRUCTURE OF THE STROMELYSIN-3 (MMP-11) CATALYTIC DOMAIN COMPLEXED WITH A PHOSPHINIC INHIBITOR

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

STROMELYSIN 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

1hv5__assembly_6__model_1

1hv5__assembly_6__model_1 | I(q)

1hv5__assembly_6__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE STROMELYSIN-3 (MMP-11) CATALYTIC DOMAIN COMPLEXED WITH A PHOSPHINIC INHIBITOR

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

STROMELYSIN 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

1hv5__assembly_6__model_1

1hv5__assembly_6__model_1 | I(q)

1hv5__assembly_6__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)