SAXSdb — 6xs8

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

Vacuolar protein sorting-associated protein 29

Chaetomium thermophilum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	48V-DTY-GLY-TYR-ASP-PRO-LEU-GLY-LEU-LYS-TYR-PHE-ALA × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0RZB5_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–203； UniProt 1–201

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	6xs8
Deposition date deposition_date	2020-07-15
Structure title title	Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic peptide RT-D3
Keywords keywords	Vps29, Retromer, Endosome, Protein transport, cyclic peptide, inhibitor, PROTEIN TRANSPORT-INHIBITOR complex; PROTEIN TRANSPORT/INHIBITOR
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.

6xs8__assembly_1__model_1

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

Download this curve (.dat)

6xs8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6xs8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.60 Å
Rg (electron density)	16.19 Å
Total Rg	17.35 Å
Atom count	1549
Residues	195
Excluded volume	27962 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6xs8__assembly_1__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	Vacuolar protein sorting-associated protein 29
Molecular weight formula_weight	22387.7 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	1755

GSMAFLILVIGNLHIPDRALDIPPKFKKLLSPGKISQTLCLGNLTDRATYDYLRSISPDLKIVRGRMDVEATSLPLMQVVTHGSLRIGFLEGFTLVSEEPDVLLAEANKLDVDVLCWAGGSHRFECFEYMDKFFVNPGSATGAFTTDWLAEGEEVVPSFCLMDVQGISLTLYVYQLRKDENGTENVAVEKVTYTKPVEPTGAS

Source Source

Source organism organism	Chaetomium thermophilum
NCBI taxonomy ID ncbi_taxonomy_id	209285
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	48V-DTY-GLY-TYR-ASP-PRO-LEU-GLY-LEU-LYS-TYR-PHE-ALA
Molecular weight formula_weight	1567.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XYGYDPLGLKYFA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	166

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Unit-cell length a length_a	47.520 Å
Unit-cell length b length_b	47.520 Å
Unit-cell length c length_c	170.990 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	41.151 Å
R factor r_factor	0.2071
R_work r_work	0.2047
R_free r_free	0.2513

Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic peptide RT-D3

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

Vacuolar protein sorting-associated protein 29

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

6xs8__assembly_1__model_1

6xs8__assembly_1__model_1 | I(q)

6xs8__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

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic peptide RT-D3

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

Vacuolar protein sorting-associated protein 29

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

6xs8__assembly_1__model_1

6xs8__assembly_1__model_1 | I(q)

6xs8__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

Entity 3 Entity 3 water

7. Citations (1)