PDBe 3kyd

X-ray diffraction
2.61Å resolution

Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic

Released:
Source organism: Homo sapiens

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
SUMO-activating enzyme subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 346 amino acids
Theoretical weight: 38.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW Q9UBE0 (Residues: 1-346; Coverage: 100%)
Gene names: AOS1, SAE1, SUA1, UBLE1A
Sequence domains: ThiF family
Structure domains: NAD(P)-binding Rossmann-like Domain
SUMO-activating enzyme subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 551 amino acids
Theoretical weight: 61.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW Q9UBT2 (Residues: 1-549; Coverage: 86%)
Gene names: HRIHFB2115, SAE2, UBA2, UBLE1B
Sequence domains:
Structure domains:
Small ubiquitin-related modifier 1 Chain: D
Molecule details ›
Chain: D
Length: 115 amino acids
Theoretical weight: 13.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW P63165 (Residues: 1-96; Coverage: 95%)
Gene names: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1
Sequence domains: Ubiquitin-2 like Rad60 SUMO-like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21212
Unit cell:
a: 101.717Å b: 115.608Å c: 90.837Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.227 0.284
Expression system: Escherichia coli