SAXSdb — 6qby

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

Tubulinyl-Tyr carboxypeptidase 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Small vasohibin-binding protein × 1 （Q8N300） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Small vasohibin-binding protein × 1 （Q8N300） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VASH2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–257； UniProt 40–295 Author chain C； PDBConstruct 2–257； UniProt 40–295

Small vasohibin-binding protein

Homo sapiens

UniProt Q8N300

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SVBP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–67； UniProt 1–66 Author chain D； PDBConstruct 2–67； UniProt 1–66

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	6qby
Deposition date deposition_date	2018-12-24
Structure title title	Crystal structure of VASH 2 in complex with SVBP
Keywords keywords	Tubulin carboxypeptidase, Cysteine protease, Complex, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6qby__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6qby__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qby__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.59 Å
Rg (electron density)	19.48 Å
Total Rg	20.41 Å
Atom count	2199
Residues	273
Excluded volume	39369 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qby__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6qby__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tubulinyl-Tyr carboxypeptidase 2
Molecular weight formula_weight	29999.1 kDa
EC 编号 ec_number	3.4.17.17
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4703

MEEDKDGGVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILGIYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTLSDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKIL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Small vasohibin-binding protein
Molecular weight formula_weight	8911.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MMDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQMQPPGEKHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

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Unit-cell length a length_a	119.887 Å
Unit-cell length b length_b	119.887 Å
Unit-cell length c length_c	102.636 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	103.830 Å
R factor r_factor	0.1920
R_work r_work	0.1900
R_free r_free	0.2300

Crystal structure of VASH 2 in complex with SVBP

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

Tubulinyl-Tyr carboxypeptidase 2

State in the Current Structure

Other States of the Same Protein in the Database

Small vasohibin-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6qby__assembly_1__model_1

6qby__assembly_1__model_1 | I(q)

6qby__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of VASH 2 in complex with SVBP

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

Tubulinyl-Tyr carboxypeptidase 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small vasohibin-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6qby__assembly_1__model_1

6qby__assembly_1__model_1 | I(q)

6qby__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)