SAXSdb — 8gkl

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

Mucin-16

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 E； UniProt 12695–12821	Fragment：SEA5 domain, residues 12695-12821	MUC16 antibody AR9.6 Fab light chain × 1 MUC16 antibody AR9.6 Fab heavy chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M PCTP pH 4.0 25% PEG 1500	Resolution 2.60 Å R-free 0.269

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 8GKL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SA9 Human MUC16 SEA5 Domain Deposited 2021-09-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12665–12857（193 aa） Fragment：SEA5 Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；ammonium acetate, PEG 10000	Resolution 1.69 Å R-free 0.216
7SA9 Human MUC16 SEA5 Domain Deposited 2021-09-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 12665–12857（193 aa） Fragment：SEA5 Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；ammonium acetate, PEG 10000	Resolution 1.69 Å R-free 0.216
8VM1 Structural Elucidation of the Mesothelin Mucin16 CA125 Interaction Deposited 2024-01-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 13475–13600（126 aa） Fragment：residues 296-359 of mesothelin (Uniprot numbering),SEA 10 domain of mucin-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Bis-Tris, NH4CL, PEG3350	Resolution 2.65 Å R-free 0.298
8VRS Mucin 16 peptide fused to MBP in complex with 4H11-scFv antibody Deposited 2024-01-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 14421–14446（26 aa） Fragment：residues 14421-14446 of mucin-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；0.1M Sodium Citrate, pH 5.0, 10mM Barium Chloride, 27% PEG MME 5000	Resolution 2.47 Å R-free 0.237
8VRS Mucin 16 peptide fused to MBP in complex with 4H11-scFv antibody Deposited 2024-01-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 14421–14446（26 aa） Fragment：residues 14421-14446 of mucin-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；0.1M Sodium Citrate, pH 5.0, 10mM Barium Chloride, 27% PEG MME 5000	Resolution 2.47 Å R-free 0.237

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

View Construct and Data Evidence

UniProt name	MUC16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–127； UniProt 12695–12821

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	8gkl
Deposition date deposition_date	2023-03-19
Structure title title	Crystal Structure of the Humanized MUC16 Specific Antibody huAR9.6
Keywords keywords	CA125, IMMUNE SYSTEM; IMMUNE SYSTEM
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	29.13 Å
Radius of gyration Rg (electron density) rg_electron	28.90 Å
Forward intensity I(0) i0	56514500.00
Molecular weight molecular_weight	58181.0 kDa
Excluded volume excluded_volume	72302 Å³
Envelope volume envelope_volume	91924 Å³
Hydration-shell volume shell_volume	28493 Å³
Envelope diameter envelope_diameter	110.2 Å
Shell Rg shell_rg	33.96 Å
Envelope Rg envelope_rg	28.91 Å
Shape Rg shape_rg	28.89 Å
Total Rg total_rg	29.41 Å
Total atoms total_atoms	4100
Residues n_residues	543
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	101.3 Å
Rg (real space) rg_real	29.35 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	5.6510e+07
I(0) uncertainty (real space) i0_real_error	8.6980e+05
Rg (reciprocal space) rg_reciprocal	29.26 Å
I(0) (reciprocal space) i0_reciprocal	56510000.0000
Solution quality estimate total_estimate	0.6355
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.9 Å
Skewness Skewness skewness	0.593
Kurtosis Kurtosis kurtosis	-0.046
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7867000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 0.092; Positv: 1.000; Valcen: 0.876; Smooth: 0.844

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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	Mucin-16
Molecular weight formula_weight	14210.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	4224

GPLLVPFTLNFTITNLKYEEDMHCPGSRKFNTTERVLQSLLGPMFKNTSVGPLYSGCRLTLLRSEKDGAATGVDAICTHRLDPKSPGVDREQLYWELSQLTNGIKELGPYTLDRNSLYVNGFTHQTS

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	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	MUC16 antibody AR9.6 Fab light chain
Molecular weight formula_weight	23884.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGHPPKLLIYGASNQGSGVPARFSGSGSGTDFSLNIHPMEEDDAAMYFCQQTKEVPWTFGGGTKVEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	MUC16 antibody AR9.6 Fab heavy chain
Molecular weight formula_weight	25216.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESGGGLVQPGGSRKLSCAASGFTFSTFGMHWVRQAPEKGLEWVAYISSGSSTIYYGDTLQGRFIISRDNPKNTLFLQMTSLRSEDTAMYYCARSGYDYDPIYYALDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGSHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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8. Citations (1)

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Unit-cell length a length_a	41.470 Å
Unit-cell length b length_b	124.360 Å
Unit-cell length c length_c	235.430 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	42.740 Å
R factor r_factor	0.2181
R_work r_work	0.2154
R_free r_free	0.2692

fit	/app/data/saxs_computation/gk/8gkl/8gkl.fit
pddf	/app/data/pr_computation/gk/8gkl/8gkl.pr.out
profile	/app/data/saxs_computation/gk/8gkl/8gkl.dat

Crystal Structure of the Humanized MUC16 Specific Antibody huAR9.6

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

Mucin-16

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 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)