SAXSdb — 1uap

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

Procollagen C-proteinase enhancer protein

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 313–442	Fragment：NTR domain	No other associated polymer	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

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 1UAP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 method 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 method 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
9EN2 Crystal structure of the metalloproteinase enhancer PCPE-1 complexed with nanobodies VHH-H4 and VHH-I5 Deposited 2024-03-12	Different construct Different oligomeric state 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 25–277（253 aa）	Not recorded	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

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 25–154； UniProt 313–442

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	1uap
Deposition date deposition_date	2003-03-14
Structure title title	NMR structure of the NTR domain from human PCOLCE1
Keywords keywords	BETA BARREL, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	14.90 Å
Radius of gyration Rg (electron density) rg_electron	14.62 Å
Forward intensity I(0) i0	1086380000.00
Molecular weight molecular_weight	280650.0 kDa
Excluded volume excluded_volume	352520 Å³
Envelope volume envelope_volume	33534 Å³
Hydration-shell volume shell_volume	16703 Å³
Envelope diameter envelope_diameter	57.8 Å
Shell Rg shell_rg	23.03 Å
Envelope Rg envelope_rg	17.38 Å
Shape Rg shape_rg	14.59 Å
Total Rg total_rg	14.87 Å
Total atoms total_atoms	39720
Residues n_residues	2620
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	50.8 Å
Rg (real space) rg_real	14.82 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.0860e+09
I(0) uncertainty (real space) i0_real_error	1.1470e+07
Rg (reciprocal space) rg_reciprocal	14.82 Å
I(0) (reciprocal space) i0_reciprocal	1086000000.0000
Solution quality estimate total_estimate	0.8599
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.184
Kurtosis Kurtosis kurtosis	-0.216
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	416400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1uapa1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.3 — TIMP-like
Family Family family	b.40.3.3 — Netrin-like domain (NTR/C345C module)

Domain ID domain_id	d1uapa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1uapA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	120 —

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8. Citations (1)

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Description description	Procollagen C-proteinase enhancer protein
Molecular weight formula_weight	16586.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	39720

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 BL21(DE3)

fit	/app/data/saxs_computation/ua/1uap/1uap.fit
pddf	/app/data/pr_computation/ua/1uap/1uap.pr.out
profile	/app/data/saxs_computation/ua/1uap/1uap.dat

NMR structure of the NTR domain from human PCOLCE1

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

Procollagen C-proteinase enhancer protein

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)