SAXSdb — 5ibk

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

S-phase kinase-associated protein 1,S-phase kinase-associated protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	F-box/WD repeat-containing protein 7 × 1 （Q969H0） Polyubiquitin-B × 1 （P0CG47） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	F-box/WD repeat-containing protein 7 × 1 （Q969H0） Polyubiquitin-B × 1 （P0CG47） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKP1_HUMAN
Isoform	P63208-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–65； UniProt 1–69 Author chain A； PDBConstruct 70–151； UniProt 82–163 Author chain D； PDBConstruct 3–65； UniProt 1–69 Author chain D； PDBConstruct 70–151； UniProt 82–163

F-box/WD repeat-containing protein 7

Homo sapiens

UniProt Q969H0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	S-phase kinase-associated protein 1,S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-B × 1 （P0CG47） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	S-phase kinase-associated protein 1,S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-B × 1 （P0CG47） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FBXW7_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–63； UniProt 263–323 Author chain E； PDBConstruct 3–63； UniProt 263–323

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	S-phase kinase-associated protein 1,S-phase kinase-associated protein 1 × 1 （P63208） F-box/WD repeat-containing protein 7 × 1 （Q969H0） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	S-phase kinase-associated protein 1,S-phase kinase-associated protein 1 × 1 （P63208） F-box/WD repeat-containing protein 7 × 1 （Q969H0） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–78； UniProt 75–150 Author chain F； PDBConstruct 3–78； UniProt 75–150

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	5ibk
Deposition date deposition_date	2016-02-22
Structure title title	Skp1-F-box in complex with a ubiquitin variant
Keywords keywords	phage display, SCF inhibitors, Fbxw7, Fbxw11, ?-Trcp, ubiquitin, PROTEIN BINDING; PROTEIN BINDING
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.

5ibk__assembly_1__model_1

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

Download this curve (.dat)

5ibk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ibk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.87 Å
Rg (electron density)	20.52 Å
Total Rg	21.38 Å
Atom count	2110
Residues	263
Excluded volume	37994 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ibk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ibk__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
Molecular weight formula_weight	16981.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	4284

GAMPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHKDDPGGSGTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	F-box/WD repeat-containing protein 7
Molecular weight formula_weight	7513.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GATQVKHMMQVIEPQFQRDFISLLPKELALYVLSFLEPKDLLQAAQTCRYWRILAEDNLLWRE

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	8811.1 kDa
Mutation mutation	L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSGSMQIFVKTGARTAITLEVEPSDTIENVKAKIQDKEGIPPDQQILIFSRKLLEDGRTLSDYNIHRESTLRLVLIFR

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 BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d5ibka1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.0 — automated matches

Domain ID domain_id	d5ibka2
Class class	a — All alpha proteins
Fold Fold fold	a.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
Family Family family	a.157.1.1 — Skp1 dimerisation domain-like

Domain ID domain_id	d5ibka3
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	d5ibkc_
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	d5ibkd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.0 — automated matches

Domain ID domain_id	d5ibkd2
Class class	a — All alpha proteins
Fold Fold fold	a.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
Family Family family	a.157.1.1 — Skp1 dimerisation domain-like

Domain ID domain_id	d5ibkf_
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

CATH v4.4 (4 domains)

Domain ID domain_id	5ibkA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	5ibkB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5ibkD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	5ibkE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	63.368 Å
Unit-cell length b length_b	98.015 Å
Unit-cell length c length_c	107.704 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.503 Å
Low-resolution limit resolution_low	47.709 Å
R factor r_factor	0.2016
R_work r_work	0.1997
R_free r_free	0.2399

Skp1-F-box in complex with a ubiquitin variant

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

S-phase kinase-associated protein 1,S-phase kinase-associated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

F-box/WD repeat-containing protein 7

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin-B

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

5ibk__assembly_1__model_1

5ibk__assembly_1__model_1 | I(q)

5ibk__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Skp1-F-box in complex with a ubiquitin variant

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

S-phase kinase-associated protein 1,S-phase kinase-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

F-box/WD repeat-containing protein 7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin-B

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

5ibk__assembly_1__model_1

5ibk__assembly_1__model_1 | I(q)

5ibk__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

CATH v4.4 (4 domains)

7. Citations (1)