1eak

Catalytic domain of proMMP-2 E404Q mutant

Method: X-RAY DIFFRACTION

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

72 KDA TYPE IV COLLAGENASE

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	INHIBITOR PEPTIDE × 1 SULFATE ION × 3 ZINC ION × 4 CALCIUM ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	INHIBITOR PEPTIDE × 1 SULFATE ION × 3 ZINC ION × 4 CALCIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MM02_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–421； UniProt 32–452 Author chain B； PDBConstruct 1–421； UniProt 32–452 Author chain C； PDBConstruct 1–421； UniProt 32–452 Author chain D； PDBConstruct 1–421； UniProt 32–452

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	1eak
Deposition date deposition_date	2001-07-12
Structure title title	Catalytic domain of proMMP-2 E404Q mutant
Keywords keywords	HYDROLASE-HYDROLASE INHIBITOR COMPLEX, HYDROLYSE, MATRIX METALLOPROTEINASE, GELATINASE A, 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.

1eak__assembly_1__model_1

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

Download this curve (.dat)

1eak__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1eak__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.26 Å
Rg (electron density)	31.99 Å
Total Rg	32.61 Å
Atom count	6702
Residues	847
Excluded volume	117480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1eak__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1eak__assembly_2__model_1`	trimeric （3）	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	72 KDA TYPE IV COLLAGENASE
Molecular weight formula_weight	47304.3 kDa
EC 编号 ec_number	3.4.24.24
Mutation mutation	YES
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	13504

SPIIKFPGDVAPKTDKELAVQYLNTFYGCPKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVANYNFFPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFCPHEALFTMGGNAEGQPCKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCVFPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLVAAHQFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPDID

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	TRICHOPLUSIA NI

Entity 2 Entity 2 polymer

Description description	INHIBITOR PEPTIDE
Molecular weight formula_weight	622.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,R

GPAGPPGA

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d1eaka1
Class class	a — All alpha proteins
Fold Fold fold	a.20 — PGBD-like
Superfamily Superfamily superfamily	a.20.1 — PGBD-like
Family Family family	a.20.1.2 — MMP N-terminal domain

Domain ID domain_id	d1eaka2
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	d1eaka3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eaka4
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eaka5
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakb1
Class class	a — All alpha proteins
Fold Fold fold	a.20 — PGBD-like
Superfamily Superfamily superfamily	a.20.1 — PGBD-like
Family Family family	a.20.1.2 — MMP N-terminal domain

Domain ID domain_id	d1eakb2
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	d1eakb3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakb4
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakb5
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakc1
Class class	a — All alpha proteins
Fold Fold fold	a.20 — PGBD-like
Superfamily Superfamily superfamily	a.20.1 — PGBD-like
Family Family family	a.20.1.2 — MMP N-terminal domain

Domain ID domain_id	d1eakc2
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	d1eakc3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakc4
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakc5
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakd1
Class class	a — All alpha proteins
Fold Fold fold	a.20 — PGBD-like
Superfamily Superfamily superfamily	a.20.1 — PGBD-like
Family Family family	a.20.1.2 — MMP N-terminal domain

Domain ID domain_id	d1eakd2
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	d1eakd3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakd4
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

Domain ID domain_id	d1eakd5
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.2 — Fibronectin type II module

CATH v4.4 (20 domains)

Domain ID domain_id	1eakA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	101 — Muramoyl-pentapeptide Carboxypeptidase; domain 1
Homologous superfamily homologous superfamily	10 — PGBD-like superfamily/PGBD

Domain ID domain_id	1eakA02
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	1eakA03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakA04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakA05
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	101 — Muramoyl-pentapeptide Carboxypeptidase; domain 1
Homologous superfamily homologous superfamily	10 — PGBD-like superfamily/PGBD

Domain ID domain_id	1eakB02
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	1eakB03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakB04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakB05
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	101 — Muramoyl-pentapeptide Carboxypeptidase; domain 1
Homologous superfamily homologous superfamily	10 — PGBD-like superfamily/PGBD

Domain ID domain_id	1eakC02
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	1eakC03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakC04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakC05
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	101 — Muramoyl-pentapeptide Carboxypeptidase; domain 1
Homologous superfamily homologous superfamily	10 — PGBD-like superfamily/PGBD

Domain ID domain_id	1eakD02
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	1eakD03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakD04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

Domain ID domain_id	1eakD05
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

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Unit-cell length a length_a	117.670 Å
Unit-cell length b length_b	166.150 Å
Unit-cell length c length_c	170.130 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	16

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

Resolution resolution	2.660 Å
Low-resolution limit resolution_low	35.580 Å
R factor r_factor	0.2710
R_work r_work	0.2710
R_free r_free	0.3030

Catalytic domain of proMMP-2 E404Q mutant

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

72 KDA TYPE IV COLLAGENASE

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

1eak__assembly_1__model_1

1eak__assembly_1__model_1 | I(q)

1eak__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer 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) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (1)

Catalytic domain of proMMP-2 E404Q mutant

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

72 KDA TYPE IV COLLAGENASE

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

1eak__assembly_1__model_1

1eak__assembly_1__model_1 | I(q)

1eak__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer 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) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (1)