SAXSdb — 3g6d

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

Interleukin-13

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 A； UniProt 21–132	Fragment：UNP residues 21-132	CNTO607 Fab Light chain × 1 CNTO607 Fab Heavy chain × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；293 K；0.1 M Sodium acetate pH 4.5, 4.9 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.263
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 21–132	Fragment：UNP residues 21-132	CNTO607 Fab Light chain × 1 CNTO607 Fab Heavy chain × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；293 K；0.1 M Sodium acetate pH 4.5, 4.9 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.263

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 3G6D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GA3 NMR STRUCTURE OF INTERLEUKIN-13 Deposited 2000-11-29	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 35–146（112 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] IL-13, 25 mM phosphate buffer, 50 mM sodium chloride, 1 mM EDTA, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
1IJZ Solution Structure of Human IL-13 Deposited 2001-05-01	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 21–132（112 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient NMR sample composition 1mM interleukin-13 U-15N; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 \| 90% H2O/10% D2O NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 \| 90% H2O/10% D2O NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl; 100% D2O; pH 6.0 \| 100% D2O	Resolution not provided
1IK0 Solution Structure of Human IL-13 Deposited 2001-05-01	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 21–132（112 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient NMR sample composition 1mM interleukin-13 U-15N; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 \| 90% H2O/10% D2O NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 \| 90% H2O/10% D2O NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl; 100% D2O; pH 6.0 \| 100% D2O	Resolution not provided
3L5W Crystal structure of the complex between IL-13 and C836 FAB Deposited 2009-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 35–146（112 aa） Fragment：UNP residues 35-146	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；0.1 M HEPES PH 7.5, 20% PEG 3350, 0.2 M SODIUM TARTRATE; CRYO CONDITIONS: MOTHER LIQUOR + 18% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.253
3L5W Crystal structure of the complex between IL-13 and C836 FAB Deposited 2009-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 35–146（112 aa） Fragment：UNP residues 35-146	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；0.1 M HEPES PH 7.5, 20% PEG 3350, 0.2 M SODIUM TARTRATE; CRYO CONDITIONS: MOTHER LIQUOR + 18% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.253
3L5X Crystal structure of the complex between IL-13 and H2L6 FAB Deposited 2009-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 35–146（112 aa） Fragment：UNP residues 35-146	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES PH 6.5, 14% PEG 3350, 0.2 M AMMONIUM TARTRATE. CRYO CONDITIONS: 0.1 M MES PH 6.5, 20% PEG 3K, 0.2 M AMM TARTRATE, 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.247
3LB6 The structure of IL-13 in complex with IL-13Ralpha2 Deposited 2010-01-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 15–146（132 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；100 mM MES, pH 6.0, 200 mM CaCl2, 20% PEG-6000, and 4% v/v polypropylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.05 Å R-free 0.269
3LB6 The structure of IL-13 in complex with IL-13Ralpha2 Deposited 2010-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 15–146（132 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；100 mM MES, pH 6.0, 200 mM CaCl2, 20% PEG-6000, and 4% v/v polypropylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.05 Å R-free 0.269
4I77 Lebrikizumab Fab bound to IL-13 Deposited 2012-11-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Z 35–146（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；15% w/v PEG1000, 0.05 M sodium malonate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.219
4PS4 Crystal structure of the complex between IL-13 and M1295 FAB Deposited 2014-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 35–146（112 aa） Fragment：UNP RESIDUES 35-146	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.1 M SODIUM ACETATE PH 4.5, 25% PEG 8K, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.271
5E4E Engineered Interleukin-13 bound to receptor Deposited 2015-10-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 34–146（113 aa） Fragment：UNP residues 34-146	Mutation：L10V, V18I, L39R, D87S, T88S, L101F, K104R, K105T	SO4 SULFATE ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；293 K；lithium sulfate, phosphate/citrate pH 4.2, PEG 1000	Resolution 3.00 Å R-free 0.288
5L6Y il13 in complex with tralokinumab Deposited 2016-06-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 35–146（112 aa）	Not recorded	FMT FORMIC ACID × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium formate	Resolution 1.99 Å R-free 0.211

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL13_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 2–113； UniProt 21–132

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	3g6d
Deposition date deposition_date	2009-02-06
Structure title title	Crystal structure of the complex between CNTO607 Fab and IL-13
Keywords keywords	IL-13, antibody, complex, epitope, Cytokine, Glycoprotein, Secreted, MONOCLONAL ANTIBODY, 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	28.96 Å
Radius of gyration Rg (electron density) rg_electron	28.65 Å
Forward intensity I(0) i0	55787700.00
Molecular weight molecular_weight	57710.0 kDa
Excluded volume excluded_volume	71859 Å³
Envelope volume envelope_volume	91899 Å³
Hydration-shell volume shell_volume	28502 Å³
Envelope diameter envelope_diameter	108.3 Å
Shell Rg shell_rg	33.69 Å
Envelope Rg envelope_rg	28.81 Å
Shape Rg shape_rg	28.59 Å
Total Rg total_rg	29.30 Å
Total atoms total_atoms	4059
Residues n_residues	539
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	104.3 Å
Rg (real space) rg_real	29.18 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	5.5790e+07
I(0) uncertainty (real space) i0_real_error	9.9100e+05
Rg (reciprocal space) rg_reciprocal	29.08 Å
I(0) (reciprocal space) i0_reciprocal	55780000.0000
Solution quality estimate total_estimate	0.8227
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.594
Kurtosis Kurtosis kurtosis	-0.023
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	12740000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.687; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.683; Smooth: 0.948

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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	CNTO607 Fab Light chain
Molecular weight formula_weight	22619.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	4059

SYELTQPPSVSVAPGQTARISCSGDNIGGTFVSWYQQKPGQAPVLVIYDDNDRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCGTWDMVTNNVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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	CNTO607 Fab Heavy chain
Molecular weight formula_weight	24461.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLVESGGGLVQPGGSLRLSCAASGFTFNSYWINWVRQAPGKGLEWVSGIAYDSSNTLYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGLGAFHWDMQPDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

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 polymer

Description description	Interleukin-13
Molecular weight formula_weight	12490.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGPVPPSTALRELIEELVNITQNQKAPLCNGSMVWSINLTAGMYCAALESLINVSGCSAIEKTQRMLSGFCPHKVSAGQFSSLHVRDTKIEVAQFVKDLLLHLKKLFREGRFN

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 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3g6da_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d3g6dh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3g6dh2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d3g6dl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3g6dl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	3g6dA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3g6dH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3g6dH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3g6dL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3g6dL02
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	66.540 Å
Unit-cell length b length_b	68.030 Å
Unit-cell length c length_c	182.350 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	3.200 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2634

fit	/app/data/saxs_computation/g6/3g6d/3g6d.fit
pddf	/app/data/pr_computation/g6/3g6d/3g6d.pr.out
profile	/app/data/saxs_computation/g6/3g6d/3g6d.dat

Crystal structure of the complex between CNTO607 Fab and IL-13

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

Interleukin-13

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 non-polymer

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)