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Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb

X-ray diffraction
1.76Å resolution
PDB entry 4k7s coloured by chain, front view.
PDB entry 4k7s coloured by chain, side view.
PDB entry 4k7s coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1
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Assembly Name: Ubiquitin
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Multimeric state: monomeric
Accessible surface area: 4212.72 Å2
Buried surface area: 372.58 Å2
Dissociation area: 105.67 Å2
Dissociation energy (ΔGdiss): 19.75 kcal/mol
Dissociation entropy (TΔSdiss): 1.56 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-143327
Monomeric assembly 1 of PDB entry 4k7s coloured by chemically distinct molecules, front view.
Monomeric assembly 1 of PDB entry 4k7s coloured by chemically distinct molecules, side view.
Monomeric assembly 1 of PDB entry 4k7s coloured by chemically distinct molecules, top view.
    Assembly 1
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA
Assembly 2
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Assembly Name: Ubiquitin
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Multimeric state: monomeric
Accessible surface area: 4354.18 Å2
Buried surface area: 373.01 Å2
Dissociation area: 95.91 Å2
Dissociation energy (ΔGdiss): 5.55 kcal/mol
Dissociation entropy (TΔSdiss): -0.37 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-143327
Monomeric assembly 2 of PDB entry 4k7s coloured by chemically distinct molecules, front view.
Monomeric assembly 2 of PDB entry 4k7s coloured by chemically distinct molecules, side view.
Monomeric assembly 2 of PDB entry 4k7s coloured by chemically distinct molecules, top view.
    Assembly 2
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA
Assembly 3 (preferred)
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Assembly Name: Ubiquitin
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Multimeric state: monomeric
Accessible surface area: 4247.95 Å2
Buried surface area: 513.85 Å2
Dissociation area: 109.52 Å2
Dissociation energy (ΔGdiss): -1.76 kcal/mol
Dissociation entropy (TΔSdiss): -0.28 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-143327
Monomeric assembly 3 of PDB entry 4k7s coloured by chemically distinct molecules, front view.
Monomeric assembly 3 of PDB entry 4k7s coloured by chemically distinct molecules, side view.
Monomeric assembly 3 of PDB entry 4k7s coloured by chemically distinct molecules, top view.
    Assembly 3
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA

Macromolecules

Ubiquitin
Chains: A, B, C
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Pfam: Ubiquitin family
InterPro:
CATH: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin in PDB entry 4k7s, assembly 3, front view.
Ubiquitin in PDB entry 4k7s, assembly 3, side view.
Ubiquitin in PDB entry 4k7s, assembly 3, top view.
PDBe-KB: UniProt Coverage View: P0CG48  
17610203040506070
 
204060MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
UniProt
P0CG48
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Sequence conservation
Molecule details ›

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