5J8P | pdb_00005j8p

Lys27-linked diubiquitin

  • Classification: PROTEIN BINDING
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2016-04-08 Released: 2016-05-18 
  • Deposition Author(s): Pan, M., Gao, S., Zheng, Y.
  • Funding Organization(s): the National Basic Research Program of China, National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.295 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of Lys27-linked diubiquitin

Pan, M., Gao, S., Zheng, Y.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ubiquitin76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62987
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D-ubiquitin76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
Entity Groups  
UniProt GroupP62987
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  17 Unique
IDChains TypeFormula2D DiagramParent
DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

DAR
Query on DAR
B
D-PEPTIDE LINKINGC6 H15 N4 O2

--

DAS
Query on DAS
B
D-PEPTIDE LINKINGC4 H7 N O4

--

DGL
Query on DGL
B
D-PEPTIDE LINKINGC5 H9 N O4

--

DGN
Query on DGN
B
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DHI
Query on DHI
B
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DIL
Query on DIL
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DLE
Query on DLE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DLY
Query on DLY
B
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DNE
Query on DNE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DPN
Query on DPN
B
D-PEPTIDE LINKINGC9 H11 N O2

--

DPR
Query on DPR
B
D-PEPTIDE LINKINGC5 H9 N O2

--

DSG
Query on DSG
B
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DSN
Query on DSN
B
D-PEPTIDE LINKINGC3 H7 N O3

--

DTH
Query on DTH
B
D-PEPTIDE LINKINGC4 H9 N O3

--

DTY
Query on DTY
B
D-PEPTIDE LINKINGC9 H11 N O3

--

DVA
Query on DVA
B
D-PEPTIDE LINKINGC5 H11 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.828α = 90
b = 63.411β = 109.16
c = 52.844γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
the National Basic Research Program of ChinaChina2013CB932800
National Natural Science Foundation of ChinaChina21532004 and 21225207

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Data collection
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2022-02-09
    Changes: Database references, Derived calculations