SAXSdb — 6vfq

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

Protocadherin-10

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	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 18–455	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 9 MAN alpha-D-mannopyranose × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；296 K；14% PEG 400 (v/v), 0.1M sodium acetate pH 4.6, 0.1M CaCl2, with 30% ethylene glycol (v/v) added as cryoprotectant	Resolution 2.30 Å R-free 0.237

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 6VFQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 18–455（438 aa） Chain C 18–455（438 aa）	Not recorded	CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection	Resolution 3.60 Å R-free 0.295
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 18–455（438 aa） Chain D 18–455（438 aa）	Not recorded	CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection	Resolution 3.60 Å R-free 0.295
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 18–455（438 aa）	Not recorded	CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection	Resolution 3.60 Å R-free 0.295
6VG4 Human protocadherin 10 ectodomain Deposited 2020-01-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–680（663 aa）	Not recorded	CA CALCIUM ION × 15 MAN alpha-D-mannopyranose × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；0.22M CaCl2, 0.1M Na Acetate pH 5.0 with 30% (v/v) glycerol as cryoprotectant and glutaraldehyde (0.5% v/v) added to the reservoir after crystal formation to aid crystal stability by cross-linking	Resolution 3.30 Å R-free 0.284
9DQV Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1 Deposited 2024-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain M 19–121（103 aa） Chain N 19–121（103 aa） Chain O 19–121（103 aa） Chain P 19–121（103 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9E96 WEEV CBA87 VLP in complex with human PCDH10-EC1 Deposited 2024-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain H 19–122（104 aa） Chain L 19–122（104 aa） Chain P 19–122（104 aa） Chain Q 19–122（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.05 Å
9L1N Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1 Deposited 2024-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric	Chain M 19–113（95 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9L41 Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human PCDH10 extracellular cadherin repeats 1-2 (EC1-EC2)(3-fold region) Deposited 2024-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain R 19–114（96 aa） Chain S 19–114（96 aa） Chain T 19–114（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCD10_HUMAN
Isoform	Q9P2E7-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 18–455

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	6vfq
Deposition date deposition_date	2020-01-06
Structure title title	Crystal structure of monomeric human protocadherin 10 EC1-EC4
Keywords keywords	;cadherin extracellular region, non-clustered delta2 family protocadherin, homophilic adhesion/recognition calcium-dependent adhesion molecule, CELL ADHESION ;; CELL ADHESION
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	51.59 Å
Radius of gyration Rg (electron density) rg_electron	54.02 Å
Forward intensity I(0) i0	36446300.00
Molecular weight molecular_weight	47941.0 kDa
Excluded volume excluded_volume	59579 Å³
Envelope volume envelope_volume	89858 Å³
Hydration-shell volume shell_volume	18453 Å³
Envelope diameter envelope_diameter	192.7 Å
Shell Rg shell_rg	37.89 Å
Envelope Rg envelope_rg	54.81 Å
Shape Rg shape_rg	54.06 Å
Total Rg total_rg	53.04 Å
Total atoms total_atoms	6506
Residues n_residues	424
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	198.7 Å
Rg (real space) rg_real	52.78 Å
Rg uncertainty (real space) rg_real_error	3.77 Å
I(0) (real space) i0_real	3.6450e+07
I(0) uncertainty (real space) i0_real_error	8.2020e+05
Rg (reciprocal space) rg_reciprocal	50.60 Å
I(0) (reciprocal space) i0_reciprocal	36340000.0000
Solution quality estimate total_estimate	0.5702
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.652
Kurtosis Kurtosis kurtosis	-0.449
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1063000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.013; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.006; Smooth: 0.368

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Protocadherin-10
Molecular weight formula_weight	48309.9 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	6658

SQLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNEKIDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLDINDNPPSFPEPDLTVEISESATPGTRFPLESAFDPDVGTNSLRDYEITPNSYFSLDVQTQGDGNRFAELVLEKPLDREQQAVHRYVLTAVDGGGGGGVGEGGGGGGGAGLPPQQQRTGTALLTIRVLDSNDNVPAFDQPVYTVSLPENSPPGTLVIQLNATDPDEGQNGEVVYSFSSHISPRARELFGLSPRTGRLEVSGELDYEESPVYQVYVQAKDLGPNAVPAHCKVLVRVLDANDNAPEISFSTVKEAVSEGAAPGTVVALFSVTDRDSEENGQVQCELLGDVPFRLKSSFKNYYTIVTEAPLDREAGDSYTLTVVARDRGEPALSTSKSIQVQVSDHHHHHH

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 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

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	9

Entity 4 Entity 4 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	man
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	144

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6vfqA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6vfqA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6vfqA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

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8. Citations (1)

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Unit-cell length a length_a	26.373 Å
Unit-cell length b length_b	78.910 Å
Unit-cell length c length_c	238.886 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	orthorhombic

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.1906
R_work r_work	0.1883
R_free r_free	0.2366

fit	/app/data/saxs_computation/vf/6vfq/6vfq.fit
pddf	/app/data/pr_computation/vf/6vfq/6vfq.pr.out
profile	/app/data/saxs_computation/vf/6vfq/6vfq.dat

Crystal structure of monomeric human protocadherin 10 EC1-EC4