SAXSdb — 2xvs

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

TETRATRICOPEPTIDE REPEAT PROTEIN 5

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 261–424	Fragment：OLIGONUCLEOTIDE-BINDING DOMAIN, RESIDUES 262-424	IOD IODIDE ION × 3 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.18M SODIUM IODIDE, 0.02M SODIUM ACETATE, 20% PEG3350, 10% ETHYLENE GLYCOL, 0.45% DMSO, 0.1M BIS-TRIS-PROPANE PH8.5	Resolution 1.80 Å R-free 0.236

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 2XVS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6T59 Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 and nascent chain-associated complex Deposited 2019-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric	Chain TT 1–440（440 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
7QWS Structure of ribosome translating beta-tubulin in complex with TTC5 and NAC Deposited 2022-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain K 1–440（440 aa）	Not recorded	ZN ZINC ION × 5 MG MAGNESIUM ION × 97	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
8BPO Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER) Deposited 2022-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric	Chain t2 1–440（440 aa）	Not recorded	MG MAGNESIUM ION × 214 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TTC5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–166； UniProt 261–424

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	2xvs
Deposition date deposition_date	2010-10-31
Structure title title	Crystal structure of human TTC5 (Strap) C-terminal OB domain
Keywords keywords	ANTITUMOR PROTEIN, P53 COFACTOR, STRESS-RESPONSE, P300; ANTITUMOR PROTEIN
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	17.59 Å
Radius of gyration Rg (electron density) rg_electron	16.07 Å
Forward intensity I(0) i0	6402410.00
Molecular weight molecular_weight	18051.0 kDa
Excluded volume excluded_volume	22443 Å³
Envelope volume envelope_volume	26313 Å³
Hydration-shell volume shell_volume	14178 Å³
Envelope diameter envelope_diameter	58.3 Å
Shell Rg shell_rg	21.55 Å
Envelope Rg envelope_rg	16.46 Å
Shape Rg shape_rg	15.99 Å
Total Rg total_rg	17.30 Å
Total atoms total_atoms	1245
Residues n_residues	165
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	57.9 Å
Rg (real space) rg_real	17.52 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	6.4020e+06
I(0) uncertainty (real space) i0_real_error	7.7720e+04
Rg (reciprocal space) rg_reciprocal	17.53 Å
I(0) (reciprocal space) i0_reciprocal	6402000.0000
Solution quality estimate total_estimate	0.8063
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.1 Å
Skewness Skewness skewness	0.238
Kurtosis Kurtosis kurtosis	-0.292
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	938000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	TETRATRICOPEPTIDE REPEAT PROTEIN 5
Molecular weight formula_weight	18182.0 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	1380

SMRQREQQLLEFLDRLTSLLESKGKVKTKKLQSMLGSLRPAHLGPCSDGHYQSASGQKVTLELKPLSTLQPGVNSGAVILGKVVFSLTTEEKVPFTFGLVDSDGPCYAVMVYNIVQSWGVLIGDSVAIPEPNLRLHRIQHKGKDYSFSSVRVETPLLLVVNGKPQG

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 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2xvsA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	550 —

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8. Citations (1)

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Unit-cell length a length_a	30.260 Å
Unit-cell length b length_b	62.390 Å
Unit-cell length c length_c	78.770 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	78.770 Å
R factor r_factor	0.1755
R_work r_work	0.1724
R_free r_free	0.2364

fit	/app/data/saxs_computation/xv/2xvs/2xvs.fit
pddf	/app/data/pr_computation/xv/2xvs/2xvs.pr.out
profile	/app/data/saxs_computation/xv/2xvs/2xvs.dat

Crystal structure of human TTC5 (Strap) C-terminal OB domain

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

TETRATRICOPEPTIDE REPEAT PROTEIN 5

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