SAXSdb — 4qxu

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

Matrix metalloproteinase-14

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 K； UniProt 218–228	Fragment：peptide (unp residues 218-228)	anti_MT1-MMP Light chain × 1 anti_MT1-MMP Heavy chain × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M (NH4)2SO4, 0.01M MgCl2 0.05M MES, 16% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.293

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 4QXU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BQQ CRYSTAL STRUCTURE OF THE MT1-MMP--TIMP-2 COMPLEX Deposited 1998-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 114–287（174 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.60	Resolution 2.75 Å R-free 0.248
1BUV CRYSTAL STRUCTURE OF THE MT1-MMP-TIMP-2 COMPLEX Deposited 1998-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 114–287（174 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.75 Å R-free 0.248
2MQS Transient Collagen Triple Helix Binding to a Key Metalloproteinase in Invasion and Development: Spin Labels to Structure Deposited 2014-06-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 316–511（196 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；310 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure ambient NMR sample composition 300 uM [U-13C; U-15N; U-2H] Hemopexin-like (HPX) of MT1-MMP, 10 mM Sodium acetate, 1 mM EDTA, 1 mM Sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.85 mM THP, 10 mM Sodium acetate, 1 mM EDTA, 1 mM Sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
3C7X Hemopexin-like domain of matrix metalloproteinase 14 Deposited 2008-02-08	Different construct 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 316–511（196 aa） Fragment：UNP residues 316-511	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；2.1M malic acid, 0.1M HCl, 40% acetone, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 1.70 Å R-free 0.207
3C7X Hemopexin-like domain of matrix metalloproteinase 14 Deposited 2008-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 316–511（196 aa） Fragment：UNP residues 316-511	Not recorded	NA SODIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；2.1M malic acid, 0.1M HCl, 40% acetone, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 1.70 Å R-free 0.207
3C7X Hemopexin-like domain of matrix metalloproteinase 14 Deposited 2008-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 316–511（196 aa） Fragment：UNP residues 316-511	Not recorded	NA SODIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；2.1M malic acid, 0.1M HCl, 40% acetone, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 1.70 Å R-free 0.207
3MA2 Complex membrane type-1 matrix metalloproteinase (MT1-MMP) with tissue inhibitor of metalloproteinase-1 (TIMP-1) Deposited 2010-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 112–292（181 aa） Fragment：Residues 112-292	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；100 mM Bis-Tris pH 5.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.05 Å R-free 0.247
3MA2 Complex membrane type-1 matrix metalloproteinase (MT1-MMP) with tissue inhibitor of metalloproteinase-1 (TIMP-1) Deposited 2010-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 112–292（181 aa） Fragment：Residues 112-292	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；100 mM Bis-Tris pH 5.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.05 Å R-free 0.247
3X23 Radixin complex Deposited 2014-12-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 563–582（20 aa） Fragment：cytoplasmic tail, UNP residues 563-582	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；12% polyethylene glycol 4000, 100mM MOPS (pH 7.0), 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.40 Å R-free 0.237
4P3C MT1-MMP:Fab complex (Form I) Deposited 2014-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 215–227（13 aa）	Not recorded	CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 12 ACT ACETATE ION × 6 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% PEG 3350, 0.2M MgCl.hexahydrate, 0.1M Hepes	Resolution 1.94 Å R-free 0.200
4P3D MT1-MMP:Fab complex (Form II) Deposited 2014-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 215–227（13 aa） Fragment：MT1-MMP V-B loop Chain M 215–227（13 aa） Fragment：MT1-MMP V-B loop	Not recorded	CL CHLORIDE ION × 2 GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% PEG 3350, 0.2M MgCl.hexahydrate, 0.1M Hepes	Resolution 1.95 Å R-free 0.210
5H0U Crystal structure of the catalytic domain of membrane type 1 matrix metalloproteinase Deposited 2016-10-07	Different construct 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 116–285（170 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Ammonium nitrate, PEG3350	Resolution 2.24 Å R-free 0.254
6CLZ MT1-MMP HPX domain with Blade 4 Loop Bound to Nanodiscs Deposited 2018-03-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 316–511（196 aa） Fragment：residues 316-511	Not recorded	PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 218 NA SODIUM ION × 1 CL CHLORIDE ION × 1	SOLUTION NMR NMR measurement conditions pH 7.2；303 K；Ionic strength (raw mmCIF value) 300；Pressure 1 NMR sample composition 20 mM Tris-HCl, 300 mM NaCl, 0.02 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 90 uM 2H, 13C, 15N MT1-MMP hemopexin-like domain, 180 uM MSP1D1, 14.4 mM PX4, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
6CM1 MT1-MMP HPX Domain with Blade 2 Loop Bound to Nanodiscs Deposited 2018-03-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 316–511（196 aa） Fragment：residues 316-511	Not recorded	PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 218 NA SODIUM ION × 1 CL CHLORIDE ION × 1	SOLUTION NMR NMR measurement conditions pH 7.2；303 K；Ionic strength (raw mmCIF value) 300；Pressure 1 NMR sample composition 20 mM Tri-HCl, 300 mM NaCl, 0.02 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 90 uM 2H, 13C, 15N MT1-MMP hemopexin-like domain, 180 uM MSP1D1, 14.4 mM PX4, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MMP14_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain K； PDBConstruct 1–11； UniProt 218–228

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	4qxu
Deposition date deposition_date	2014-07-22
Structure title title	Novel Inhibition Mechanism of Membrane Metalloprotease by an Exosite-Swiveling Conformational antibody
Keywords keywords	Structural Genomics, PSI-2, Protein Structure Initiative, Israel Structural Proteomics Center, ISPC, Igg fold, IMMUNE SYSTEM; IMMUNE SYSTEM
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	25.77 Å
Radius of gyration Rg (electron density) rg_electron	24.64 Å
Forward intensity I(0) i0	41168700.00
Molecular weight molecular_weight	48751.0 kDa
Excluded volume excluded_volume	60473 Å³
Envelope volume envelope_volume	74279 Å³
Hydration-shell volume shell_volume	25377 Å³
Envelope diameter envelope_diameter	82.7 Å
Shell Rg shell_rg	31.64 Å
Envelope Rg envelope_rg	24.37 Å
Shape Rg shape_rg	24.61 Å
Total Rg total_rg	25.48 Å
Total atoms total_atoms	3429
Residues n_residues	450
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	79.9 Å
Rg (real space) rg_real	25.77 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	4.1170e+07
I(0) uncertainty (real space) i0_real_error	5.7780e+05
Rg (reciprocal space) rg_reciprocal	25.77 Å
I(0) (reciprocal space) i0_reciprocal	41170000.0000
Solution quality estimate total_estimate	0.9073
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.526
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7527000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.912

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	anti_MT1-MMP Light chain
Molecular weight formula_weight	24124.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3458

DVLMTQTPLSLPVGLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHAPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	anti_MT1-MMP Heavy chain
Molecular weight formula_weight	24995.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVKLVESGGGLVKPGGSLKLSCAASGFIFSNYAMSWVRQTPEKRLEWVATISGGGRNIYSLDSVKGRFTFFRDNARNTLYLQMSSLRSEDTAMYFCSRENYGSSFTYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCAAALEHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Matrix metalloproteinase-14
Molecular weight formula_weight	1330.4 kDa
EC 编号 ec_number	3.4.24.80
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

AEPWTVRNEDL

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	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4qxuh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4qxul1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4qxul2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	4qxuH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4qxuH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4qxuL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4qxuL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	79.560 Å
Unit-cell length b length_b	79.560 Å
Unit-cell length c length_c	93.600 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	4

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.260 Å
R factor r_factor	0.2457
R_work r_work	0.2431
R_free r_free	0.2934

fit	/app/data/saxs_computation/qx/4qxu/4qxu.fit
pddf	/app/data/pr_computation/qx/4qxu/4qxu.pr.out
profile	/app/data/saxs_computation/qx/4qxu/4qxu.dat

Novel Inhibition Mechanism of Membrane Metalloprotease by an Exosite-Swiveling Conformational antibody

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

Matrix metalloproteinase-14

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)