SAXSdb — 6fzw

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

Collagen alpha-1(III) chain

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1185–1466 Chain B； UniProt 1185–1466 Chain C； UniProt 1185–1466	Not recorded	Procollagen C-endopeptidase enhancer 1 × 1 （Q15113） 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

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 6FZW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V53 Crystal structure of a SPARC-collagen complex Deposited 2008-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 564–584（21 aa） Fragment：RESIDUES 564-584 Chain C 564–584（21 aa） Fragment：RESIDUES 564-584 Chain D 564–584（21 aa） Fragment：RESIDUES 564-584	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 3.20 Å R-free 0.320
3DMW Crystal structure of human type III collagen G982-G1023 containing C-terminal cystine knot Deposited 2008-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1158–1199（42 aa） Fragment：UNP residues 1158-1199 Chain B 1158–1199（42 aa） Fragment：UNP residues 1158-1199 Chain C 1158–1199（42 aa） Fragment：UNP residues 1158-1199	Mutation：Q1183M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Q1183M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Q1183M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；30% PEG 550, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.274
4AE2 Crystal structure of Human fibrillar procollagen type III C- propeptide trimer Deposited 2012-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain B 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain C 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466	Mutation：YES Mutation：YES Mutation：YES	CA CALCIUM ION × 3 NO3 NITRATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% PEG 3350, 0.1 M BIS TRIS PROPANE PH 6.5, POTASSIUM NITRATE 0.2 M	Resolution 1.68 Å R-free 0.214
4AEJ Crystal structure of Human fibrillar procollagen type III C- propeptide trimer Deposited 2012-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain B 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain C 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 3 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions 20% PEG 3350, 0.2 M NACL	Resolution 2.21 Å R-free 0.237
4AK3 Crystal structure of Human fibrillar procollagen type III C- propeptide trimer Deposited 2012-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1222–1466（245 aa） Fragment：CPROPEPTIDE, RESIDUES 1222-1466	Mutation：YES	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.337
6FZV Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (short) Deposited 2018-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1222–1466（245 aa） Chain B 1222–1466（245 aa） Chain C 1222–1466（245 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
7WWR Structure of a triple-helix region of human collagen type III from Trautec Deposited 2022-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 973–1002（30 aa） Chain B 973–1002（30 aa） Chain C 973–1002（30 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MIB pH5.0, 25% PEG 1500	Resolution 1.30 Å R-free 0.194
7WWS Structure of a triple-helix region of human collagen type III from Trautec Deposited 2022-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 976–1002（27 aa） Chain B 976–1002（27 aa） Chain C 976–1002（27 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M MgAc2, 0.1M Na cacodylate pH6.5, 20% PEG 8000	Resolution 1.30 Å R-free 0.158
7XAN Structure of a triple-helix region of human collagen type III from Trautec Deposited 2022-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 922–948（27 aa） Chain B 922–948（27 aa） Chain C 922–948（27 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.04M K phosphate monobasic, 16% w/v PEG 8000, 20% v/v Glycerol	Resolution 1.50 Å R-free 0.200

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CO3A1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–293； UniProt 1185–1466 Author chain B； PDBConstruct 12–293； UniProt 1185–1466 Author chain C； PDBConstruct 12–293； UniProt 1185–1466

Procollagen C-endopeptidase enhancer 1

Homo sapiens

UniProt Q15113

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 26–278	Not recorded	Collagen alpha-1(III) chain × 3 （P02461） 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

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 6FZW	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 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
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 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	2
Chains and sequence ranges	Author chain D； PDBConstruct 5–257； UniProt 26–278

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	6fzw
Deposition date deposition_date	2018-03-15
Structure title title	Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (long)
Keywords keywords	Collagen, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	34.45 Å
Radius of gyration Rg (electron density) rg_electron	34.03 Å
Forward intensity I(0) i0	157171000.00
Molecular weight molecular_weight	98445.0 kDa
Excluded volume excluded_volume	122090 Å³
Envelope volume envelope_volume	159880 Å³
Hydration-shell volume shell_volume	40994 Å³
Envelope diameter envelope_diameter	118.9 Å
Shell Rg shell_rg	38.87 Å
Envelope Rg envelope_rg	34.14 Å
Shape Rg shape_rg	34.07 Å
Total Rg total_rg	34.23 Å
Total atoms total_atoms	13459
Residues n_residues	886
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	112.8 Å
Rg (real space) rg_real	34.44 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	1.5720e+08
I(0) uncertainty (real space) i0_real_error	2.8610e+06
Rg (reciprocal space) rg_reciprocal	34.45 Å
I(0) (reciprocal space) i0_reciprocal	157200000.0000
Solution quality estimate total_estimate	0.8977
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.7 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17850000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.902

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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	Collagen alpha-1(III) chain
Molecular weight formula_weight	31997.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	13459

ETGHHHHHHSAGPPGPPGAPGPCCGGVGAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQQITYHCKNSIAYMDQASGNVKKALKLMGSNEGEFKAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIGGPDQEFGVDVGPVCFL

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	Procollagen C-endopeptidase enhancer 1
Molecular weight formula_weight	28696.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

APLAQTPNYTRPVFLCGGDVKGESGYVASEGFPNLYPPNKECIWTITVPEGQTVSLSFRVFDLELHPACRYDALEVFAGSGTSGQRLGRFCGTFRPAPLVAPGNQVTLRMTTDEGTGGRGFLLWYSGRATSGTEHQFCGGRLEKAQGTLTTPNWPESDYPPGISCSWHIIAPPDQVIALTFEKFDLEPDTYCRYDSVSVFNGAVSDDSRRLGKFCGDAVPGSISSEGNELLVQFVSDLSVTADGFSASYKTLPRGTAAAHHHHHH

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 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	5

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	3

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6fzwd1
Class class	b — All beta proteins
Fold Fold fold	b.23 — CUB-like
Superfamily Superfamily superfamily	b.23.1 — Spermadhesin, CUB domain
Family Family family	b.23.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	6fzwA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1000 —

Domain ID domain_id	6fzwB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1000 —

Domain ID domain_id	6fzwC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1000 —

Domain ID domain_id	6fzwD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	290 — Spermadhesin, CUB domain

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8. Citations (1)

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Unit-cell length a length_a	88.880 Å
Unit-cell length b length_b	143.650 Å
Unit-cell length c length_c	156.710 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	12

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

Resolution resolution	2.780 Å
Low-resolution limit resolution_low	68.787 Å
R factor r_factor	0.2486
R_work r_work	0.2474
R_free r_free	0.2712

fit	/app/data/saxs_computation/fz/6fzw/6fzw.fit
pddf	/app/data/pr_computation/fz/6fzw/6fzw.pr.out
profile	/app/data/saxs_computation/fz/6fzw/6fzw.dat

Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (long)

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

Collagen alpha-1(III) chain

State in the Current Structure

Other States of the Same Protein in the Database

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)