PDBe 6byh

X-ray diffraction
2.61Å resolution

Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex.

Released:

Function and Biology Details

Reaction catalysed:
(1a) protein N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2)
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
S-phase kinase-associated protein 1 Chains: A, B, G
Molecule details ›
Chains: A, B, G
Length: 165 amino acids
Theoretical weight: 18.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63208 (Residues: 1-163; Coverage: 100%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
Lysine-specific demethylase 2A Chains: E, F, I
Molecule details ›
Chains: E, F, I
Length: 47 amino acids
Theoretical weight: 5.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2K7 (Residues: 888-932; Coverage: 4%)
Gene names: CXXC8, FBL7, FBXL11, JHDM1A, KDM2A, KIAA1004
Ubiquitin Chains: C, D, H
Molecule details ›
Chains: C, D, H
Length: 87 amino acids
Theoretical weight: 9.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 152-163, 164-228; Coverage: 34%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: P212121
Unit cell:
a: 60.56Å b: 118.188Å c: 146.336Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.235 0.294
Expression system: Escherichia coli