5XPK | pdb_00005xpk

Crystal structure of ubiquitin-k6mimic

• PDB DOI: https://doi.org/10.2210/pdb5XPK/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-06-03 Released: 2017-07-19 
• Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.310 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Literature

Structure of ubiquitin-k6mimic at 2.27 Angstroms resolution.

Man, P., Shuai, G., Qian, Q., Lei, L.

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: 17.16 kDa 
• Atom Count: 1,217 
• Modeled Residue Count: 152 
• 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  Gene Names: UBB
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	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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLZ	A	L-PEPTIDE LINKING	C5 H12 N2 O2 S		LYS
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		--
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		--
MED	B	D-PEPTIDE LINKING	C5 H11 N O2 S		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.310 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.656	α = 90
b = 46.626	β = 91.47
c = 40.495	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

Revision History  

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary