› 5xpk

X-ray diffraction
2.27Å resolution

Crystal structure of ubiquitin-k6mimic

Released:
DOI: 10.2210/pdb5xpk/pdb
PDB entry 5xpk coloured by chain, front view.
PDB entry 5xpk coloured by chain, side view.
PDB entry 5xpk coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Man P, Shuai G, Qian Q, Lei L

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143232 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin Chain: A
Molecule details ›
Chain: A
Length: 76 amino acids
Theoretical weight: 8.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

No bound ligands
18 modified residues:
Ligand SLZ 1 x SLZ
Ligand MED 1 x MED
Ligand DGN 6 x DGN
Ligand DIL 7 x DIL
Ligand DPN 2 x DPN
Ligand DVA 4 x DVA
Ligand DLY 7 x DLY
Ligand DTH 7 x DTH
Ligand DLE 9 x DLE
Ligand DGL 6 x DGL
Ligand DPR 3 x DPR
Ligand DSN 3 x DSN
Ligand DAS 5 x DAS
Ligand DSG 2 x DSG
Ligand DAL 2 x DAL
Ligand DAR 4 x DAR
Ligand DTY 1 x DTY
Ligand DHI 1 x DHI

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P2
Unit cell:
a: 26.656Å b: 46.626Å c: 40.495Å
α: 90° β: 91.47° γ: 90°
R-values:
R R work R free
0.254 0.25 0.31
Expression systems:
  • Escherichia coli K-12
  • Not provided

Quick links