5J8P

Lys27-linked diubiquitin

  • Classification: PROTEIN BINDING
  • Organism(s): Homo sapiens

  • 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: 1.554 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ubiquitin
A
76Homo sapiensMutation(s): 0 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-ubiquitin
B
76Homo sapiensMutation(s): 0 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  17 Unique
IDChainsTypeFormula2D DiagramParent
DIL
Query on DIL
B
D-PEPTIDE LINKINGC6 H13 N O2

--

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

--

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

--

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

--

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

--

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

--

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

--

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

--

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

--

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

--

DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

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

--

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

--

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

--

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

--

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

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.554 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 44.828α = 90.00
b = 63.411β = 109.16
c = 52.844γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Data collection
  • Version 1.2: 2017-10-18
    Type: Author supporting evidence, Derived calculations