SAXSdb — 3wwq

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

Ubiquitin

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Fanconi anemia-associated protein of 20 kDa × 1 （Q6NZ36） ZINC ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Fanconi anemia-associated protein of 20 kDa × 1 （Q6NZ36） ZINC ION × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Fanconi anemia-associated protein of 20 kDa × 1 （Q6NZ36） ZINC ION × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Fanconi anemia-associated protein of 20 kDa × 1 （Q6NZ36） ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_MOUSE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain G； PDBConstruct 1–76； UniProt 1–76 Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76 Author chain K； PDBConstruct 1–76； UniProt 1–76

Fanconi anemia-associated protein of 20 kDa

Homo sapiens

UniProt Q6NZ36

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin × 1 （P0CG50） Ubiquitin × 1 （P0CG50） ZINC ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin × 1 （P0CG50） Ubiquitin × 1 （P0CG50） ZINC ION × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin × 1 （P0CG50） Ubiquitin × 1 （P0CG50） ZINC ION × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin × 1 （P0CG50） Ubiquitin × 1 （P0CG50） ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FAP20_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 6–44； UniProt 142–180 Author chain F； PDBConstruct 6–44； UniProt 142–180 Author chain I； PDBConstruct 6–44； UniProt 142–180 Author chain L； PDBConstruct 6–44； UniProt 142–180

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	3wwq
Deposition date deposition_date	2014-06-23
Structure title title	Crystal structure of FAAP20 UBZ domain in complex with Lys63-linked diubiquitin
Keywords keywords	protein complex, DNA repair, PROTEIN BINDING-METAL BINDING PROTEIN complex; PROTEIN BINDING/METAL BINDING PROTEIN
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.

3wwq__assembly_1__model_1

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

Download this curve (.dat)

3wwq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wwq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.49 Å
Rg (electron density)	18.54 Å
Total Rg	19.36 Å
Atom count	1499
Residues	189
Excluded volume	26834 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wwq__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wwq__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3wwq__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3wwq__assembly_4__model_1`	trimeric （3）	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	Ubiquitin
Molecular weight formula_weight	8604.8 kDa
Mutation mutation	K63R
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	6359

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8691.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGD

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Fanconi anemia-associated protein of 20 kDa
Molecular weight formula_weight	4849.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

GPGHMAALRSCPMCQKEFAPRLTQLDVDSHLAQCLAESTEDVTW

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

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	346

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3wwqa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wwqb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wwqd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wwqe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wwqg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wwqh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wwqj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wwqk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

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Unit-cell length a length_a	59.767 Å
Unit-cell length b length_b	45.850 Å
Unit-cell length c length_c	172.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.06 °
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	1.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2096
R_work r_work	0.2082
R_free r_free	0.2346

Crystal structure of FAAP20 UBZ domain in complex with Lys63-linked diubiquitin

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Fanconi anemia-associated protein of 20 kDa

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

3wwq__assembly_1__model_1

3wwq__assembly_1__model_1 | I(q)

3wwq__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

Crystal structure of FAAP20 UBZ domain in complex with Lys63-linked diubiquitin

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fanconi anemia-associated protein of 20 kDa

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

3wwq__assembly_1__model_1

3wwq__assembly_1__model_1 | I(q)

3wwq__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)