SAXSdb — 5k3q

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

Tripartite motif-containing protein 5,Tripartite motif-containing protein 5

Macaca mulatta

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 NITRATE ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRIM5_MACMU
Isoform	Q0PF16-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–64； UniProt 94–154 Author chain A； PDBConstruct 69–101； UniProt 229–261 Author chain B； PDBConstruct 4–64； UniProt 94–154 Author chain B； PDBConstruct 69–101； UniProt 229–261 Author chain C； PDBConstruct 4–64； UniProt 94–154 Author chain C； PDBConstruct 69–101； UniProt 229–261 Author chain D； PDBConstruct 4–64； UniProt 94–154 Author chain D； PDBConstruct 69–101； UniProt 229–261

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	5k3q
Deposition date deposition_date	2016-05-19
Structure title title	Rhesus macaques Trim5alpha Bbox2 domain
Keywords keywords	Zinc finger Bbox2 Antiretroviral, LIGASE; LIGASE
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.

5k3q__assembly_1__model_1

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

Download this curve (.dat)

5k3q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5k3q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	13.88 Å
Rg (electron density)	12.73 Å
Total Rg	13.77 Å
Atom count	682
Residues	86
Excluded volume	11954 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5k3q__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5k3q__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 (4)

Entity 1 Entity 1 polymer

Description description	Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
Molecular weight formula_weight	11746.5 kDa
EC 编号 ec_number	6.3.2.-,6.3.2.-
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	1466

GPGVDHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKGGDPYMRELISELEHRLQGSMMDLLQGVDGIIKRIEN

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus macaque
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5k3qa_
Class class	g — Small proteins
Fold Fold fold	g.43 — B-box zinc-binding domain
Superfamily Superfamily superfamily	g.43.1 — B-box zinc-binding domain
Family Family family	g.43.1.0 — automated matches

Domain ID domain_id	d5k3qb1
Class class	g — Small proteins
Fold Fold fold	g.43 — B-box zinc-binding domain
Superfamily Superfamily superfamily	g.43.1 — B-box zinc-binding domain
Family Family family	g.43.1.0 — automated matches

Domain ID domain_id	d5k3qb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5k3qc_
Class class	g — Small proteins
Fold Fold fold	g.43 — B-box zinc-binding domain
Superfamily Superfamily superfamily	g.43.1 — B-box zinc-binding domain
Family Family family	g.43.1.0 — automated matches

Domain ID domain_id	d5k3qd_
Class class	g — Small proteins
Fold Fold fold	g.43 — B-box zinc-binding domain
Superfamily Superfamily superfamily	g.43.1 — B-box zinc-binding domain
Family Family family	g.43.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5k3qA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	5k3qB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	5k3qC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	5k3qD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

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Unit-cell length a length_a	30.751 Å
Unit-cell length b length_b	54.556 Å
Unit-cell length c length_c	54.479 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	38.250 Å
R factor r_factor	0.1801
R_work r_work	0.1774
R_free r_free	0.2291

Rhesus macaques Trim5alpha Bbox2 domain

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

Tripartite motif-containing protein 5,Tripartite motif-containing protein 5

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

5k3q__assembly_1__model_1

5k3q__assembly_1__model_1 | I(q)

5k3q__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Rhesus macaques Trim5alpha Bbox2 domain

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

Tripartite motif-containing protein 5,Tripartite motif-containing protein 5

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

5k3q__assembly_1__model_1

5k3q__assembly_1__model_1 | I(q)

5k3q__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)