SAXSdb — 6tqr

▼

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

Vesicle-associated membrane protein-associated protein A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 3 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	StAR-related lipid transfer protein 3 × 1 （Q14849） water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 2 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	StAR-related lipid transfer protein 3 × 1 （Q14849） CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAPA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–205； UniProt 8–212 Author chain B； PDBConstruct 1–205； UniProt 8–212 Author chain C； PDBConstruct 1–205； UniProt 8–212 Author chain D； PDBConstruct 1–205； UniProt 8–212

StAR-related lipid transfer protein 3

OrganismNot specified

UniProt Q14849

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
2	Protein heterocomplex	Heteromer	Protein 2	Vesicle-associated membrane protein-associated protein A × 1 （Q9P0L0） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Vesicle-associated membrane protein-associated protein A × 1 （Q9P0L0） CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STAR3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–17； UniProt 200–216 Author chain F； PDBConstruct 1–17； UniProt 200–216

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6tqr
Deposition date deposition_date	2019-12-17
Structure title title	The crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3.
Keywords keywords	Membrane contact sites, FFAT motif, MSP domain, Endoplasmic reticulum, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6tqr__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6tqr__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6tqr__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	17.29 Å
Rg (electron density)	16.10 Å
Total Rg	17.05 Å
Atom count	1003
Residues	126
Excluded volume	18005 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6tqr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6tqr__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6tqr__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6tqr__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Vesicle-associated membrane protein-associated protein A
Molecular weight formula_weight	24478.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4579

MAKHEQILVLDPPTDLKFKGPFTDVVTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGSTVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNTSDMEAVWKEAKPDELMDSKLRCVFEMPNENDKLNDMEPSKAVPLNASKQDGPMPKPHSVSLNDTETRKLMEECKRLQGEMMKLSEENRHLRDEGLRLRKVAHSDKPALEHHHHH

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(DE3)

Entity 2 Entity 2 polymer

Description description	StAR-related lipid transfer protein 3
Molecular weight formula_weight	1983.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

GALSEGQFYSPPESFAG

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	287

▶

Unit-cell length a length_a	39.140 Å
Unit-cell length b length_b	43.780 Å
Unit-cell length c length_c	83.640 Å
Unit-cell angle α angle_alpha	89.46 °
Unit-cell angle β angle_beta	92.91 °
Unit-cell angle γ angle_gamma	105.13 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	42.260 Å
R factor r_factor	0.2068
R_work r_work	0.2043
R_free r_free	0.2543

The crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3.

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

Vesicle-associated membrane protein-associated protein A

State in the Current Structure

Other States of the Same Protein in the Database

StAR-related lipid transfer protein 3

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

6tqr__assembly_3__model_1

6tqr__assembly_3__model_1 | I(q)

6tqr__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

The crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3.

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

Vesicle-associated membrane protein-associated protein A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

StAR-related lipid transfer protein 3

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

6tqr__assembly_3__model_1

6tqr__assembly_3__model_1 | I(q)

6tqr__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)