SAXSdb — 9en2

▼

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

Procollagen C-endopeptidase enhancer 1

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 25–277	Not recorded	VHH-H4 × 1 VHH-I5 × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；292.15 K；10% PEG 8000, 50 mM L-argininamide dihydrochloride, 50 mM spermine, 50 mM sodium cacodylate pH 6.5, 50 mM potassium chloride	Resolution 2.20 Å R-free 0.242

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 9EN2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1UAP NMR structure of the NTR domain from human PCOLCE1 Deposited 2003-03-14	Different construct 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 313–442（130 aa） Fragment：NTR domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；301 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR measurement conditions pH 7.5；301 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 1mM NTR(PCOLCE1) U-15N \| 90% H2O/10% D2O NMR sample composition 1mM NTR(PCOLCE1) \| 90% H2O/10% D2O NMR sample composition 1mM NTR(PCOLCE1) \| 100% D2O	Resolution not provided
6FZV Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (short) Deposited 2018-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 26–278（253 aa）	Not recorded	CA CALCIUM ION × 5 FLC CITRATE ANION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20 mg/ml protein in 20 mM HEPES pH 7.5, 180 mM NaCl, 2.5 mM calcium chloride; 0.2 M potassium citrate, 16% PEG3350	Resolution 2.70 Å R-free 0.258
6FZW Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (long) Deposited 2018-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 26–278（253 aa）	Not recorded	CA CALCIUM ION × 5 FLC CITRATE ANION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20 mg/ml protein in 20 mM HEPES pH 7.5, 180 mM NaCl, 2.5 mM calcium chloride; 0.2 M ammonium citrate, 18% PEG3350	Resolution 2.78 Å R-free 0.271

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCOC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 47–299； UniProt 25–277

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9en2
Deposition date deposition_date	2024-03-12
Structure title title	Crystal structure of the metalloproteinase enhancer PCPE-1 complexed with nanobodies VHH-H4 and VHH-I5
Keywords keywords	COLLAGEN, STRUCTURAL PROTEIN, EXTRACELLULAR MATRIX, FIBROSIS, NANOBODIES, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.04 Å
Radius of gyration Rg (electron density) rg_electron	25.06 Å
Forward intensity I(0) i0	47695200.00
Molecular weight molecular_weight	52018.0 kDa
Excluded volume excluded_volume	64368 Å³
Envelope volume envelope_volume	80607 Å³
Hydration-shell volume shell_volume	26750 Å³
Envelope diameter envelope_diameter	82.1 Å
Shell Rg shell_rg	32.44 Å
Envelope Rg envelope_rg	24.81 Å
Shape Rg shape_rg	25.04 Å
Total Rg total_rg	25.94 Å
Total atoms total_atoms	3658
Residues n_residues	478
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

▼

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

Maximum dimension Dmax dmax	79.5 Å
Rg (real space) rg_real	25.93 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	4.7700e+07
I(0) uncertainty (real space) i0_real_error	5.9270e+05
Rg (reciprocal space) rg_reciprocal	25.97 Å
I(0) (reciprocal space) i0_reciprocal	47700000.0000
Solution quality estimate total_estimate	0.9159
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.9 Å
Skewness Skewness skewness	0.126
Kurtosis Kurtosis kurtosis	-0.617
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6912000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.982

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Procollagen C-endopeptidase enhancer 1
Molecular weight formula_weight	32437.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4036

MGILPSPGMPALLSLVSLLSVLLMGCVAETGHHHHHHLEVLFQGPAGQTPNYARPVFLCGGDVKGESGYVASEGFPNLYPPNKECIWTITVPEGQTVSLSFRVFDLELHPACRYDALEVFAGSGTSGQRLGRFCGTFRPAPLVAPGNQVTLRMTTDEGTGGRGFLLWYSGRATSGTEHQFCGGRLEKAQGTLTTPNWPESDYPPGISCSWHIIAPPDQVIALTFEKFDLEPDTYCRYDSVSVFNGAVSDDSRRLGKFCGDAVPGSISSEGNELLVQFVSDLSVTADGFSASYKTLPRGTLGT

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	VHH-H4
Molecular weight formula_weight	16608.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKYLLPTAAAGLLLLAAQPAMAEVQLQASGGGFVQPGGSLRLSCAASGFTSEISNMGWFRQAPGKEREFVSAISGTHTTQTYYADSVKGRFTISRDNSKNTVYLQMNSLRAEDTATYYCAAEQDMSDLWLGSYWGQGTQVTVSSAAAHHHHHHG

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	VHH-I5
Molecular weight formula_weight	15628.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKYLLPTAAAGLLLLAAQPAMAQVQLVESGGGLVQPGGFLRLLCTASGNIFSSNTMGWYRRAPGKQREWVASISKGGSTNYADSVKDRFTISRSITKNTVYLQMVNLKPEDTAVYYCNPVPDSDNYASGQGTQVTVSSHHHHHH

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	365

▶

8. Citations (1)

▶

Unit-cell length a length_a	54.830 Å
Unit-cell length b length_b	95.945 Å
Unit-cell length c length_c	110.771 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	2.200 Å
Low-resolution limit resolution_low	49.000 Å
R factor r_factor	—
R_work r_work	0.2083
R_free r_free	0.2422

fit	/app/data/saxs_computation/en/9en2/9en2.fit
pddf	/app/data/pr_computation/en/9en2/9en2.pr.out
profile	/app/data/saxs_computation/en/9en2/9en2.dat

Crystal structure of the metalloproteinase enhancer PCPE-1 complexed with nanobodies VHH-H4 and VHH-I5

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

Procollagen C-endopeptidase enhancer 1

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

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)