SAXSdb — 5iml

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

V-set and immunoglobulin domain-containing protein 4

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 19–232	Fragment：UNP residues 19-232	Nanobody × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；(1) 1.2M sodium citrate tribasic dehydrate, 0.1M BIS-TRIS propane pH7.0 and (2) 0.17M Ammonium sulfate, 15% Glycerol, 25.5% PEG 4000	Resolution 1.80 Å R-free 0.226

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 5IML	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ICC Extracellular Domain of CRIg Deposited 2006-09-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–137（119 aa） Fragment：extracellular domain of CRIG	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.4；298 K；pH 6.4, EVAPORATION, temperature 298K	Resolution 1.20 Å R-free 0.172
2ICE CRIg bound to C3c Deposited 2006-09-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain S 19–137（119 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å R-free 0.295
2ICE CRIg bound to C3c Deposited 2006-09-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain T 19–137（119 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å R-free 0.295
2ICF CRIg bound to C3b Deposited 2006-09-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 19–137（119 aa）	Not recorded	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；pH 6.5, EVAPORATION, temperature 293K	Resolution 4.10 Å R-free 0.330
5IMK Nanobody targeting human Vsig4 in Spacegroup C2 Deposited 2016-03-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 19–232（214 aa） Fragment：UNP residues 19-232	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium citrate tribasic dehydrate pH5.6, 20% 2-Propanol, 20% PEG 4000	Resolution 1.23 Å R-free 0.185
8TE5 Crystal structure of a multiple lysine-to-arginine substitution mutant of the human CRIg C3b-binding domain Deposited 2023-07-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–137（118 aa）	Mutation：K15R,K36R,K62R,K72R,K110R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium aaetate (pH 6.5) 0.2 M ammonium acetate 30% (w/v) peg-4000	Resolution 1.50 Å R-free 0.223
8TE6 Crystal structure of a multiple lysine-to-arginine substitution mutant of the human CRIg C3b-binding domain Deposited 2023-07-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–137（118 aa）	Mutation：K15R,K36R,K62R,K72R,K110R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium acetate (pH 6.5) 0.2 M ammonium acetate 30% (w/v) PEG-4000	Resolution 1.25 Å R-free 0.196
9EZH Structure of single-domain antibody VHH_h4 in complex with human Vsig4 Deposited 2024-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–137（118 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0,1M Bis-Tris pH 6.0 and 24% PEG3350	Resolution 1.94 Å R-free 0.239
9EZI Structure of single-domain antibody VHH_h5 in complex with human Vsig4 Deposited 2024-04-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–137（118 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0,1M Bis-Tris pH 6.5 and 30% PEG3350	Resolution 1.97 Å R-free 0.243
9EZU Structure of the single-domain antibody VHH_h1 in complex with human Vsig4 Deposited 2024-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–137（118 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0,17M ammonium sulfate 15% glycerol 25,5% PEG 4000	Resolution 1.05 Å R-free 0.176
9EZV Structure of the single-domain antibody VHH_h2 in complex with human Vsig4 Deposited 2024-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–137（118 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8 IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；287 K；0,1M Na-citrate pH 5,6 20% 2-propanol 21% PEG 4000	Resolution 1.45 Å R-free 0.215
9EZW Structure of the single-domain antibody VHH_h3 in complex with human Vsig4 Deposited 2024-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–137（118 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；294 K；0,1M Na-citrate pH 5,6 20% 2-propanol 21% PEG 4000	Resolution 1.90 Å R-free 0.228
9EZW Structure of the single-domain antibody VHH_h3 in complex with human Vsig4 Deposited 2024-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 20–137（118 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；294 K；0,1M Na-citrate pH 5,6 20% 2-propanol 21% PEG 4000	Resolution 1.90 Å R-free 0.228
9EZW Structure of the single-domain antibody VHH_h3 in complex with human Vsig4 Deposited 2024-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 20–137（118 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；294 K；0,1M Na-citrate pH 5,6 20% 2-propanol 21% PEG 4000	Resolution 1.90 Å R-free 0.228
9EZW Structure of the single-domain antibody VHH_h3 in complex with human Vsig4 Deposited 2024-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 20–137（118 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；294 K；0,1M Na-citrate pH 5,6 20% 2-propanol 21% PEG 4000	Resolution 1.90 Å R-free 0.228

11 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VSIG4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–220； UniProt 19–232

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	5iml
Deposition date deposition_date	2016-03-06
Structure title title	Nanobody targeting human Vsig4 in Spacegroup P212121
Keywords keywords	Nanobody, Complement Receptor, Vsig4 CRIg, 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	20.52 Å
Radius of gyration Rg (electron density) rg_electron	19.82 Å
Forward intensity I(0) i0	13982500.00
Molecular weight molecular_weight	27207.0 kDa
Excluded volume excluded_volume	33667 Å³
Envelope volume envelope_volume	39592 Å³
Hydration-shell volume shell_volume	17492 Å³
Envelope diameter envelope_diameter	73.4 Å
Shell Rg shell_rg	25.27 Å
Envelope Rg envelope_rg	20.14 Å
Shape Rg shape_rg	19.78 Å
Total Rg total_rg	20.71 Å
Total atoms total_atoms	3762
Residues n_residues	244
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	72.1 Å
Rg (real space) rg_real	20.57 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.3980e+07
I(0) uncertainty (real space) i0_real_error	1.7810e+05
Rg (reciprocal space) rg_reciprocal	20.56 Å
I(0) (reciprocal space) i0_reciprocal	13980000.0000
Solution quality estimate total_estimate	0.8547
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.9 Å
Skewness Skewness skewness	0.429
Kurtosis Kurtosis kurtosis	-0.260
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5195000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	V-set and immunoglobulin domain-containing protein 4
Molecular weight formula_weight	24606.8 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	3940

HHHHHHGRPILEVPESVTGPWKGDVNLPCTYDPLQGYTQVLVKWLVQRGSDPVTIFLRDSSGDHIQQAKYQGRLHVSHKVPGDVSLQLSTLEMDDRSHYTCEVTWQTPDGNQVVRDKITELRVQKLSVSKPTVTTGSGYGFTVPQGMRISLQCQARGSPPISYIWYKQQTNNQEPIKVATLSTLLFKPAVIADSGSYFCTAKGQVGSEQHSDIVKFVVKD

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

Entity 2 Entity 2 polymer

Description description	Nanobody
Molecular weight formula_weight	14599.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLVESGGGLVQAGGSLRLSCAASGRTFSSYGMGWFRQAPGKEREFVAAIRWNGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAGRWDKYGSSFQDEYDYWGQGTQVTVSSHHHHHH

来源 Source

来源生物 organism	Camelidae
NCBI Class编号 ncbi_taxonomy_id	9835
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5imlA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5imlB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	29.269 Å
Unit-cell length b length_b	50.048 Å
Unit-cell length c length_c	160.648 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	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	47.780 Å
R factor r_factor	0.1852
R_work r_work	0.1811
R_free r_free	0.2261

fit	/app/data/saxs_computation/im/5iml/5iml.fit
pddf	/app/data/pr_computation/im/5iml/5iml.pr.out
profile	/app/data/saxs_computation/im/5iml/5iml.dat

Nanobody targeting human Vsig4 in Spacegroup P212121

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

V-set and immunoglobulin domain-containing protein 4

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)