3VON

Crystalstructure of the ubiquitin protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report



Literature

Molecular basis of K63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13

Sato, Y.Yamagata, A.Goto-Ito, S.Kubota, K.Miyamoto, K.Nakada, S.Fukai, S.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin thioesterase OTUB1A, H, O, V, c, j228Homo sapiensMutation(s): 0 
Gene Names: HSPC263OTB1OTU1OTUB1
EC: 3.4.19.12
Find proteins for Q96FW1 (Homo sapiens)
Explore Q96FW1 
Go to UniProtKB:  Q96FW1
NIH Common Fund Data Resources
PHAROS  Q96FW1
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 variant 2B, D, F, I, K, M, P, R, T, W, Y, a, d, f, h, k, m, o138Homo sapiensMutation(s): 0 
Gene Names: MMS2UBE2V2UEV2
Find proteins for Q15819 (Homo sapiens)
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Go to UniProtKB:  Q15819
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PHAROS  Q15819
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 NC, E, G, J, L, N, Q, S, U, X, Z, b, e, g, i, l, n, p148Homo sapiensMutation(s): 0 
Gene Names: BLUUbc13UBE2N
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
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PHAROS  P61088
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.064α = 90
b = 137.285β = 90.03
c = 257.109γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-01-30 
  • Released Date: 2012-05-30 
  • Deposition Author(s): Sato, Y., Fukai, S.

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release