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2g4d

Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SENP1 protein

Homo sapiens

UniProt Q9P0U3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Small ubiquitin-related modifier 1 × 1 （P63165） water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Small ubiquitin-related modifier 1 × 1 （P63165） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2ckg 2ckg 2xph 2xph 2xre 2xre

6 assemblies

Homodimer
2iyc 2xre 2xre

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2ckh 2g4d 2g4d 2iy0 2iy1 2iy1 2iyd 6nnq

8 assemblies

View Construct and Data Evidence
UniProt name SENP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–205； UniProt 440–643 Author chain C； PDBConstruct 1–205； UniProt 440–643

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 2 SENP1 protein × 1 （Q9P0U3） water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 SENP1 protein × 1 （Q9P0U3） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1a5r 2mw5 2n1v 5b7a 5elj 5ghd 6j4i

7 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1tgz 1tgz 1wyw 1y8r 1y8r 1z5s 2asq 2bf8 2g4d 2g4d 2io2 2iy0

87 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SUMO1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–78； UniProt 20–97 Author chain D； PDBConstruct 1–78； UniProt 20–97

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_id2g4d
Deposition date deposition_date2006-02-22
Structure title titleCrystal structure of human SENP1 mutant (C603S) in complex with SUMO-1
Keywords keywordsprotease, ubiquitin-like protein, SUMO maturation, SUMO deconjugation, Hydrolase-PROTEIN BINDING COMPLEX; Hydrolase/PROTEIN BINDING
Experimental Method methodX-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.

2g4d__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2g4d__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2g4d__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.19 Å
Rg (electron density)19.14 Å
Total Rg20.11 Å
Atom count2331
Residues283
Excluded volume41647 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2g4d__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2g4d__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 (3)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2g4da1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.7 — Adenain-like
Domain ID domain_idd2g4db_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd2g4dc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.7 — Adenain-like
Domain ID domain_idd2g4dd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (4 domains)

Domain ID domain_id2g4dA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily10 — Adenoviral Proteinase; Chain A
Domain ID domain_id2g4dB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2g4dC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily10 — Adenoviral Proteinase; Chain A
Domain ID domain_id2g4dD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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7. Citations (2)