SAXSdb — 5tth

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

C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1

Streptococcus pyogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	ADENOSINE-5'-DIPHOSPHATE × 2 BERYLLIUM TRIFLUORIDE ION × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8WFV1_DANRE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 7–653； UniProt 73–719 Author chain B； PDBConstruct 7–653； UniProt 73–719

C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1

Streptococcus pyogenes

UniProt Q8G9G1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	ADENOSINE-5'-DIPHOSPHATE × 2 BERYLLIUM TRIFLUORIDE ION × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8G9G1_STRPY
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 656–738； UniProt 461–543 Author chain B； PDBConstruct 660–672； UniProt 550–562

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	5tth
Deposition date deposition_date	2016-11-03
Structure title title	Heterodimeric SpyCatcher/SpyTag-fused zebrafish TRAP1 in ATP/ADP-hybrid state
Keywords keywords	;Hsp90, ATP, Chaperone, Trap1, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG ;; CHAPERONE
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.

5tth__assembly_1__model_1

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

Download this curve (.dat)

5tth__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tth__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.04 Å
Rg (electron density)	41.81 Å
Total Rg	41.91 Å
Atom count	10415
Residues	1292
Excluded volume	185330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tth__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 (5)

Entity 1 Entity 1 polymer

Description description	C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1
Molecular weight formula_weight	83827.7 kDa
Mutation mutation	I734E and M769Y
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	10447

GIDPFTSTQQHTEPAEEETLHNIITDTENVQGSFSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNGSDALEKLRHRMITAGGDTAPMEIHLQTDSVKGTFTIQDTGVGMNKEDLVSNLGTIARSGSKAFLDALQNQAEASSSIIGQFGVGFYSAFMVADKVEVYSQSAEADAPGYKWSSDGSGVFEVAEASGVRQGTKIVLHLKDDCKEFSSEDRVKEVVTKYSNFVSFPIFLNGRRLNTLQALWMMEPKDISEWQHEEFYRYVAQAYDKPRYTLHYRADAPLNIRSIFYVPEMKPSMFDVSREMGSSVALYSRKILIQTKATDILPKWLRFLRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRVIRFLLDQSKKDPEKYARFFEDYGLFMREGIVTTGEQSVKEDIAKLLRFESSALPAGQQTSLMEYSSRMKAGTRNIYYLCAPNRHLAEHSPYFEAMKQKDMEVLFCFEQFDELTLLHLREFDRKKLISAETDIVVDHYKEEKFQDSKPASERLSSEQAEDLLAWMRNALVQRVTNIKVTPRLDTHPAMITVLEMGAARHFLRTQQLARSSEERAQILQPTLEINTGHDLIKKLHALKDSNPELAQLLLEQIYDNAMIAAGLNEDPRPMISRLNQLLTRALEKHGSDSATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAAPDGYEVATAITFTVNEQGQVTVNG

Source Source

Source organism organism	Streptococcus pyogenes
NCBI taxonomy ID ncbi_taxonomy_id	1314
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	C-terminal Spytag fusion of R417A zebrafish TNF receptor-associated protein 1
Molecular weight formula_weight	76439.7 kDa
Mutation mutation	R417A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GIDPFTSTQQHTEPAEEETLHNIITDTENVQGSFSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNGSDALEKLRHRMITAGGDTAPMEIHLQTDSVKGTFTIQDTGVGMNKEDLVSNLGTIARSGSKAFLDALQNQAEASSSIIGQFGVGFYSAFMVADKVEVYSQSAEADAPGYKWSSDGSGVFEVAEASGVRQGTKIVLHLKDDCKEFSSEDRVKEVVTKYSNFVSFPIFLNGRRLNTLQALWMMEPKDISEWQHEEFYRYVAQAYDKPRYTLHYRADAPLNIRSIFYVPEMKPSMFDVSREMGSSVALYSRKILIQTKATDILPKWLRFLRGVVDSEDIPLNLSAELLQESALIRKLRDVLQQRVIRFLLDQSKKDPEKYARFFEDYGLFMREGIVTTGEQSVKEDIAKLLRFESSALPAGQQTSLMEYSSRMKAGTRNIYYLCAPNRHLAEHSPYFEAMKQKDMEVLFCFEQFDELTLLHLREFDRKKLISAETDIVVDHYKEEKFQDSKPASERLSSEQAEDLLAWMRNALVQRVTNIKVTPRLDTHPAMITVLEMGAARHFLRTQQLARSSEERAQILQPTLEINTGHDLIKKLHALKDSNPELAQLLLEQIYDNAMIAAGLNEDPRPMISRLNQLLTRALEKHGGSGSSAHIVMVDAYKPTK

Source Source

Source organism organism	Streptococcus pyogenes
NCBI taxonomy ID ncbi_taxonomy_id	1314
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	5tthA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	5tthA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	5tthA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11260 —

Domain ID domain_id	5tthA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	790 — Heat shock protein 90, C-terminal domain

Domain ID domain_id	5tthA05
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	180.086 Å
Unit-cell length b length_b	95.711 Å
Unit-cell length c length_c	126.558 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	134.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	49.000 Å
R factor r_factor	0.2299
R_work r_work	0.2284
R_free r_free	0.2610

Heterodimeric SpyCatcher/SpyTag-fused zebrafish TRAP1 in ATP/ADP-hybrid state

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

C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1

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

5tth__assembly_1__model_1

5tth__assembly_1__model_1 | I(q)

5tth__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

Heterodimeric SpyCatcher/SpyTag-fused zebrafish TRAP1 in ATP/ADP-hybrid state

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

C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1

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

5tth__assembly_1__model_1

5tth__assembly_1__model_1 | I(q)

5tth__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)