5JBV | pdb_00005jbv

Lys27-linked triubiquitin

• PDB DOI: https://doi.org/10.2210/pdb5JBV/pdb

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


• Deposited: 2016-04-13 Released: 2016-05-18 
• Deposition Author(s): Pan, M., Gao, S., Zheng, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.306 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.268 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Literature

Structure of Lys27-linked triubiquitin

Pan, M., Gao, S., Zheng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.27 kDa 
• Atom Count: 1,243 
• Modeled Residue Count: 147 
• Deposited Residue Count: 152 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ubiquitin	B	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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	C [auth A], D [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.306 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.268 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.758	α = 90
b = 51.758	β = 90
c = 138.252	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Pan, M., Gao, S., Zheng, Y.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection, Derived calculations
• Version 1.2: 2022-02-09
  Changes: Database references