1eak

Catalytic domain of proMMP-2 E404Q mutant

Method: X-RAY DIFFRACTION D_max: 175.7 Å Quality: REASONABLE

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 32–452 Chain C； UniProt 32–452	Fragment：CATALYTIC DOMAIN RESIDUES 32-452 Mutation：YES	INHIBITOR PEPTIDE × 1 SO4 SULFATE ION × 3 ZN ZINC ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；PH 8.50	Resolution 2.66 Å R-free 0.303
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 32–452 Chain D； UniProt 32–452	Fragment：CATALYTIC DOMAIN RESIDUES 32-452 Mutation：YES	INHIBITOR PEPTIDE × 1 SO4 SULFATE ION × 3 ZN ZINC ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；PH 8.50	Resolution 2.66 Å R-free 0.303

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1EAK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CK7 GELATINASE A (FULL-LENGTH) Deposited 1999-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–660（631 aa） Fragment：FULL-LENGTH	Mutation：E404A	ZN ZINC ION × 2 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.8	Resolution 2.80 Å R-free 0.327
1CXW THE SECOND TYPE II MODULE FROM HUMAN MATRIX METALLOPROTEINASE 2 Deposited 1999-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 278–336（59 aa） Fragment：THE SECOND TYPE II MODULE	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR measurement conditions pH 5.1；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition 1.3MM COL-2 NA; 90% H2O, 10% D2O NMR sample composition 1.3MM COL-2 NA; D2O NMR sample composition 1MM COL-2 U-15N; 90% H2O, 10% D2O NMR sample composition 4MM COL-2 U-15N; 90% H2O, 10% D2O	Resolution not provided
1GEN C-TERMINAL DOMAIN OF GELATINASE A Deposited 1995-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 443–660（218 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.260
1GXD proMMP-2/TIMP-2 complex Deposited 2002-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 30–660（631 aa）	Mutation：YES	SO4 SULFATE ION × 1 ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.50	Resolution 3.10 Å R-free 0.333
1GXD proMMP-2/TIMP-2 complex Deposited 2002-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–660（631 aa）	Mutation：YES	SO4 SULFATE ION × 1 ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.50	Resolution 3.10 Å R-free 0.333
1HOV SOLUTION STRUCTURE OF A CATALYTIC DOMAIN OF MMP-2 COMPLEXED WITH SC-74020 Deposited 2000-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–256（147 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 2 I52 N-{4-[(1-HYDROXYCARBAMOYL-2-METHYL-PROPYL)-(2-MORPHOLIN-4-YL-ETHYL)-SULFAMOYL]-4-PENTYL-BENZAMIDE × 1	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.3-0.4mM U-15N, 13C MMP-2C: unlabeled SC-74020 in 20mM TRIS-d11-HCl, 5mM CaCl2, 10uM ZnCl2, 20uM unlabeled SC-74020 \| 90% H2O/10% D2O	Resolution not provided
1J7M The Third Fibronectin Type II Module from Human Matrix Metalloproteinase 2 Deposited 2001-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 337–394（58 aa） Fragment：third fibronectin type II module	Mutation：E11G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.4；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5mM col-3 NA; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM col-3 NA; D2O \| D2O NMR sample composition 1mM col-3 U-15n; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1KS0 The First Fibronectin Type II Module from Human Matrix Metalloproteinase 2 Deposited 2002-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 223–282（60 aa） Fragment：First Fibronectin Type II Module	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5mM col-1; 90% H2O, 10% d6-acetone \| 90% H2O, 10% d6-acetone NMR sample composition 0.5mM col-1; 90% D2O, 10% d6-acetone \| 90% D2O, 10% d6-acetone NMR sample composition 0.7mM col-1 15N; 90% H2O, 10% d6-acetone \| 90% H2O, 10% d6-acetone	Resolution not provided
1QIB CRYSTAL STRUCTURE OF GELATINASE A CATALYTIC DOMAIN Deposited 1999-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–213（99 aa） Fragment：CATALYTIC DOMAIN RESIDUES 88-250 WITH THE FIBRONECTIN DOMAIN DELETED Chain A 394–449（56 aa） Fragment：CATALYTIC DOMAIN RESIDUES 88-250 WITH THE FIBRONECTIN DOMAIN DELETED	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.80 Å R-free 0.244
1RTG C-TERMINAL DOMAIN (HAEMOPEXIN-LIKE DOMAIN) OF HUMAN MATRIX METALLOPROTEINASE-2 Deposited 1995-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 451–660（210 aa） Fragment：C-TERMINAL RESIDUES 451 - 660, HAEMOPEXIN-LIKE DOMAIN	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
3AYU Crystal structure of MMP-2 active site mutant in complex with APP-drived decapeptide inhibitor Deposited 2011-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–219（110 aa） Fragment：UNP residues 110-219 and 394-450 Chain A 394–450（57 aa） Fragment：UNP residues 110-219 and 394-450	Mutation：E108K, Q110V, E121A Mutation：E108K, Q110V, E121A	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.205

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.03 Å
Radius of gyration Rg (electron density) rg_electron	52.04 Å
Forward intensity I(0) i0	576486000.00
Molecular weight molecular_weight	190760.0 kDa
Excluded volume excluded_volume	234780 Å³
Envelope volume envelope_volume	342760 Å³
Hydration-shell volume shell_volume	61453 Å³
Envelope diameter envelope_diameter	182.0 Å
Shell Rg shell_rg	46.87 Å
Envelope Rg envelope_rg	51.48 Å
Shape Rg shape_rg	52.03 Å
Total Rg total_rg	51.89 Å
Total atoms total_atoms	13395
Residues n_residues	1693
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	175.7 Å
Rg (real space) rg_real	51.61 Å
Rg uncertainty (real space) rg_real_error	1.80 Å
I(0) (real space) i0_real	5.7650e+08
I(0) uncertainty (real space) i0_real_error	1.0950e+07
Rg (reciprocal space) rg_reciprocal	50.55 Å
I(0) (reciprocal space) i0_reciprocal	575700000.0000
Solution quality estimate total_estimate	0.7352
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.7 Å
Skewness Skewness skewness	0.645
Kurtosis Kurtosis kurtosis	-0.267
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	40760000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.625; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.572; Smooth: 0.106

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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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7. 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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8. Citations (1)

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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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 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

7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ea/1eak/1eak.fit
pddf	/app/data/pr_computation/ea/1eak/1eak.pr.out
profile	/app/data/saxs_computation/ea/1eak/1eak.dat