5XDP | pdb_00005xdp

K11/48-branched teraubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

K11/48-branched teraubiquitin

Liang, L., Gao, S.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-ubiquitinA [auth B]76Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ubiquitin-BB [auth A]76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  17 Unique
IDChains TypeFormula2D DiagramParent
DAL
Query on DAL		A [auth B]D-PEPTIDE LINKINGC3 H7 N O2

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DAR
Query on DAR		A [auth B]D-PEPTIDE LINKINGC6 H15 N4 O2

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DAS
Query on DAS		A [auth B]D-PEPTIDE LINKINGC4 H7 N O4

--

DGL
Query on DGL		A [auth B]D-PEPTIDE LINKINGC5 H9 N O4

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DGN
Query on DGN		A [auth B]D-PEPTIDE LINKINGC5 H10 N2 O3

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DHI
Query on DHI		A [auth B]D-PEPTIDE LINKINGC6 H10 N3 O2

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DIL
Query on DIL		A [auth B]D-PEPTIDE LINKINGC6 H13 N O2

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DLE
Query on DLE		A [auth B]D-PEPTIDE LINKINGC6 H13 N O2

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DLY
Query on DLY		A [auth B]D-PEPTIDE LINKINGC6 H14 N2 O2

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DNE
Query on DNE		A [auth B]D-PEPTIDE LINKINGC6 H13 N O2

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DPN
Query on DPN		A [auth B]D-PEPTIDE LINKINGC9 H11 N O2

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DPR
Query on DPR		A [auth B]D-PEPTIDE LINKINGC5 H9 N O2

--

DSG
Query on DSG		A [auth B]D-PEPTIDE LINKINGC4 H8 N2 O3

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DSN
Query on DSN		A [auth B]D-PEPTIDE LINKINGC3 H7 N O3

--

DTH
Query on DTH		A [auth B]D-PEPTIDE LINKINGC4 H9 N O3

--

DTY
Query on DTY		A [auth B]D-PEPTIDE LINKINGC9 H11 N O3

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DVA
Query on DVA		A [auth B]D-PEPTIDE LINKINGC5 H11 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.938α = 103.03
b = 26.163β = 94.16
c = 46.54γ = 99.65
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description