SAXSdb — 2iy0

▼

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

SENTRIN-SPECIFIC PROTEASE 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	SMALL UBIQUITIN-RELATED MODIFIER 1 × 1 （P63165） RAN GTPASE-ACTIVATING PROTEIN 1 × 1 （P46060） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SENP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–174； UniProt 419–592 Author chain A； PDBConstruct 176–226； UniProt 593–643

SMALL UBIQUITIN-RELATED MODIFIER 1

HOMO SAPIENS

UniProt P63165

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SENTRIN-SPECIFIC PROTEASE 1 × 1 （Q9P0U3） RAN GTPASE-ACTIVATING PROTEIN 1 × 1 （P46060） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUMO1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–82； UniProt 20–101

RAN GTPASE-ACTIVATING PROTEIN 1

HOMO SAPIENS

UniProt P46060

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SENTRIN-SPECIFIC PROTEASE 1 × 1 （Q9P0U3） SMALL UBIQUITIN-RELATED MODIFIER 1 × 1 （P63165） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RGP1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–156； UniProt 432–587

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2iy0
Deposition date deposition_date	2006-07-11
Structure title title	SENP1 (mutant) SUMO1 RanGAP
Keywords keywords	;HYDROLASE-HYDROLASE ACTIVATOR COMPLEX, HYDROLASE-ACTIVATOR COMPLEX, PROTEASE, HYDROLASE, UBIQUITIN, THIOL PROTEASE, LEUCINE- RICH REPEAT, UBL CONJUGATION PATHWAY, PROTEIN PROTEIN COMPLEX, GTPASE ACTIVATION, HYDROLASE-ACTIVATOR COMPLEX UBL CONJUGATION, NUCLEAR PROTEIN, PHOSPHORYLATION ;; HYDROLASE/HYDROLASE ACTIVATOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2iy0__assembly_1__model_1

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

Download this curve (.dat)

2iy0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iy0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.54 Å
Rg (electron density)	24.66 Å
Total Rg	25.59 Å
Atom count	3709
Residues	458
Excluded volume	66644 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iy0__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	SENTRIN-SPECIFIC PROTEASE 1
Molecular weight formula_weight	26900.1 kDa
EC 编号 ec_number	3.4.22.-
Mutation mutation	YES
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	3715

EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDAGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

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 2 Entity 2 polymer

Description description	SMALL UBIQUITIN-RELATED MODIFIER 1
Molecular weight formula_weight	9524.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV

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 3 Entity 3 polymer

Description description	RAN GTPASE-ACTIVATING PROTEIN 1
Molecular weight formula_weight	17141.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2iy0a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.7 — Adenain-like

Domain ID domain_id	d2iy0b_
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.15.1.0 — automated matches

Domain ID domain_id	d2iy0c1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.12 — Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
Family Family family	a.118.12.1 — Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	2iy0A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily	10 — Adenoviral Proteinase; Chain A

Domain ID domain_id	2iy0B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2iy0C00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	200 — Ran-GTPase activating protein 1, C-terminal domain

▶

Unit-cell length a length_a	83.380 Å
Unit-cell length b length_b	83.380 Å
Unit-cell length c length_c	148.044 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.770 Å
Low-resolution limit resolution_low	37.350 Å
R factor r_factor	0.2300
R_work r_work	0.2280
R_free r_free	0.2790

SENP1 (mutant) SUMO1 RanGAP

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

SENTRIN-SPECIFIC PROTEASE 1

State in the Current Structure

Other States of the Same Protein in the Database

SMALL UBIQUITIN-RELATED MODIFIER 1

State in the Current Structure

Other States of the Same Protein in the Database

RAN GTPASE-ACTIVATING 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

2iy0__assembly_1__model_1

2iy0__assembly_1__model_1 | I(q)

2iy0__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

SENP1 (mutant) SUMO1 RanGAP

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

SENTRIN-SPECIFIC PROTEASE 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

SMALL UBIQUITIN-RELATED MODIFIER 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

RAN GTPASE-ACTIVATING 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

2iy0__assembly_1__model_1

2iy0__assembly_1__model_1 | I(q)

2iy0__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)