5JBY | pdb_00005jby

Lys27-linked triubiquitin

• PDB DOI: https://doi.org/10.2210/pdb5JBY/pdb

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


• Deposited: 2016-04-14 Released: 2016-07-20 
• Deposition Author(s): Pan, M., Gao, S., Zheng, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.308 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Structure of Lys27-linked triubiquitin

Pan, M., Gao, S., Zheng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.43 kDa 
• Atom Count: 3,573 
• Modeled Residue Count: 419 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin	A, C, E	76	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ubiquitin	B, D, F	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987 GTEx:  ENSG00000221983

Small Molecules

Modified Residues  17 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	B, D, F	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	B, D, F	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DAS	B, D, F	D-PEPTIDE LINKING	C4 H7 N O4		--
DGL	B, D, F	D-PEPTIDE LINKING	C5 H9 N O4		--
DGN	B, D, F	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DHI	B, D, F	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DIL	B, D, F	D-PEPTIDE LINKING	C6 H13 N O2		--
DLE	B, D, F	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	B, D, F	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DNE	B, D, F	D-PEPTIDE LINKING	C6 H13 N O2		--
DPN	B, D, F	D-PEPTIDE LINKING	C9 H11 N O2		--
DPR	B, D, F	D-PEPTIDE LINKING	C5 H9 N O2		--
DSG	B, D, F	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DSN	B, D, F	D-PEPTIDE LINKING	C3 H7 N O3		--
DTH	B, D, F	D-PEPTIDE LINKING	C4 H9 N O3		--
DTY	B, D, F	D-PEPTIDE LINKING	C9 H11 N O3		--
DVA	B, D, F	D-PEPTIDE LINKING	C5 H11 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.308 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.758	α = 90.02
b = 51.749	β = 118.15
c = 54.977	γ = 119.95

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Pan, M., Gao, S., Zheng, Y.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references, Derived calculations