SAXSdb — 1c7k

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

ZINC ENDOPROTEASE

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–132	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIQUID DIFFUSION；pH 7；277 K；acetone, pH 7.0, LIQUID DIFFUSION, temperature 277K	Resolution 1.00 Å R-free 0.178

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 1C7K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KUH ZINC PROTEASE FROM STREPTOMYCES CAESPITOSUS Deposited 1996-02-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–132（132 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.225
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–132（131 aa） Fragment：Mature protease Chain C 2–132（131 aa） Fragment：Mature protease	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.242
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 2–132（131 aa） Fragment：Mature protease Chain G 2–132（131 aa） Fragment：Mature protease	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.242
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 2–132（131 aa） Fragment：Mature protease Chain K 2–132（131 aa） Fragment：Mature protease	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.242

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SNPA_STRCS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 1–132

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	1c7k
Deposition date deposition_date	2000-02-19
Structure title title	CRYSTAL STRUCTURE OF THE ZINC PROTEASE
Keywords keywords	alpha and beta protein, METALLOPROTEINASE, HYDROLASE; HYDROLASE
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	14.88 Å
Radius of gyration Rg (electron density) rg_electron	13.58 Å
Forward intensity I(0) i0	4989640.00
Molecular weight molecular_weight	14477.0 kDa
Excluded volume excluded_volume	17402 Å³
Envelope volume envelope_volume	19346 Å³
Hydration-shell volume shell_volume	12057 Å³
Envelope diameter envelope_diameter	45.6 Å
Shell Rg shell_rg	19.40 Å
Envelope Rg envelope_rg	13.86 Å
Shape Rg shape_rg	13.57 Å
Total Rg total_rg	14.71 Å
Total atoms total_atoms	1017
Residues n_residues	132
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	47.4 Å
Rg (real space) rg_real	14.77 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	4.9900e+06
I(0) uncertainty (real space) i0_real_error	5.1360e+04
Rg (reciprocal space) rg_reciprocal	14.78 Å
I(0) (reciprocal space) i0_reciprocal	4990000.0000
Solution quality estimate total_estimate	0.8884
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.370
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	846800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ZINC ENDOPROTEASE
Molecular weight formula_weight	14387.3 kDa
EC 编号 ec_number	3.4.24.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1133

TVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG

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	1

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c7ka_
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.92.1.1 — Zinc protease

CATH v4.4 (1 domains)

Domain ID domain_id	1c7kA00
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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8. Citations (4)

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Unit-cell length a length_a	55.103 Å
Unit-cell length b length_b	55.199 Å
Unit-cell length c length_c	37.243 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	1.000 Å
Low-resolution limit resolution_low	55.000 Å
R factor r_factor	0.1480
R_work r_work	—
R_free r_free	0.1780

fit	/app/data/saxs_computation/c7/1c7k/1c7k.fit
pddf	/app/data/pr_computation/c7/1c7k/1c7k.pr.out
profile	/app/data/saxs_computation/c7/1c7k/1c7k.dat

CRYSTAL STRUCTURE OF THE ZINC PROTEASE

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

ZINC ENDOPROTEASE

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