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6hg7

Crystal structure of a collagen II fragment containing the binding site of PEDF and COMP, (POG)4-LKG HRG FTG LQG-POG(4)

Method: X-RAY DIFFRACTION Dmax: 113.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Collagen alpha-1(II) chain

OrganismNot specified

UniProt P02458

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1116–1153 Chain B； UniProt 1116–1153 Chain C； UniProt 1116–1153 Fragment：C-terminal PEDF/COMP binding region of collagen II Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；298 K；1.5 M Ammonium sulphate and 0.1 M BIS-TRIS propane pH 7.0 Resolution 1.00 Å R-free 0.187

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 6HG7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1U5M Structure of a Chordin-like Cysteine-rich Repeat (VWC module) from Collagen IIA Deposited 2004-07-28 Different construct Different mutation/modification 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 25–97（73 aa） Fragment：Exon2
Mutation：T67A, T71A, S73A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM potassium phosphate；Pressure ambient
NMR sample composition 0.8mM U-15N exon2; 50mM phosphate buffer; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8mM U-15N exon2; 50mM phosphate buffer; 0.02% NaN3; 99.9% D2O | 99.9% D2O
NMR sample composition 0.8mM U-15N,13C exon2; 50mM phosphate buffer; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2FSE Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1 (DRB1*0101), complexed with the immunodominant determinant of human type II collagen Deposited 2006-01-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 392–405（14 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% polyethylene glycol 3,350 and 200 mM ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.295
2FSE Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1 (DRB1*0101), complexed with the immunodominant determinant of human type II collagen Deposited 2006-01-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 392–405（14 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% polyethylene glycol 3,350 and 200 mM ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.295
2SEB X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II Deposited 1997-10-16 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 E 1169–1178（10 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.1 M NA ACETATE PH 4.6 9 - 14% PEG 4000 0.2 M AMMONIUM ACETATE
Resolution 2.50 Å R-free 0.280
5NIR Crystal structure of collagen 2A vWC domain Deposited 2017-03-27 Different construct Different mutation/modification 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 29–98（70 aa）
Not recorded EDO 1,2-ETHANEDIOL × 7 PEG DI(HYDROXYETHYL)ETHER × 2 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M HEPES, pH 7.5, 40% PEG 200
Resolution 1.74 Å R-free 0.231
5NIR Crystal structure of collagen 2A vWC domain Deposited 2017-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 29–98（70 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 5 PG4 TETRAETHYLENE GLYCOL × 3 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M HEPES, pH 7.5, 40% PEG 200
Resolution 1.74 Å R-free 0.231
7NZE Crystal structure of HLA-DR4 in complex with a human collagen type II peptide Deposited 2021-03-24 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 EEE 459–473（15 aa）
Chain FFF 459–473（15 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；290 K；20% polyethylene glycol 3350 and 200 mM ammonium chloride
Resolution 2.05 Å R-free 0.245

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CO2A1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–38； UniProt 1116–1153 Author chain B； PDBConstruct 1–38； UniProt 1116–1153 Author chain C； PDBConstruct 1–38； UniProt 1116–1153

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6hg7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6hg7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6hg7
Deposition date deposition_date2018-08-22
Structure title titleCrystal structure of a collagen II fragment containing the binding site of PEDF and COMP, (POG)4-LKG HRG FTG LQG-POG(4)
Keywords keywordscollagen helix, collagen-like peptide, collagen II, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.25 Å
Radius of gyration Rg (electron density) rg_electron30.07 Å
Forward intensity I(0) i02171360.00
Molecular weight molecular_weight10479.0 kDa
Excluded volume excluded_volume12974 ų
Envelope volume envelope_volume17061 ų
Hydration-shell volume shell_volume7348 ų
Envelope diameter envelope_diameter111.9 Å
Shell Rg shell_rg25.18 Å
Envelope Rg envelope_rg31.18 Å
Shape Rg shape_rg29.96 Å
Total Rg total_rg29.71 Å
Total atoms total_atoms1429
Residues n_residues84
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax113.4 Å
Rg (real space) rg_real29.56 Å
Rg uncertainty (real space) rg_real_error2.18 Å
I(0) (real space) i0_real2.1710e+06
I(0) uncertainty (real space) i0_real_error4.2110e+04
Rg (reciprocal space) rg_reciprocal29.16 Å
I(0) (reciprocal space) i0_reciprocal2171000.0000
Solution quality estimate total_estimate0.5926
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary10.1 Å
Skewness Skewness skewness0.716
Kurtosis Kurtosis kurtosis-0.240
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52330.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.004; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.003; Smooth: 0.687
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)