5X3M | pdb_00005x3m

crystal structure of p-Ub-S65-NH2

• PDB DOI: https://doi.org/10.2210/pdb5X3M/pdb

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


• Deposited: 2017-02-06 Released: 2017-04-05 
• Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.271 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structure of p-Ub-S65-NH2 at 1.82 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.25 kDa 
• Atom Count: 1,374 
• Modeled Residue Count: 149 
• Deposited Residue Count: 152 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	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 [auth D]	76	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  18 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
DAL	B [auth D]	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	B [auth D]	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DAS	B [auth D]	D-PEPTIDE LINKING	C4 H7 N O4		--
DGL	B [auth D]	D-PEPTIDE LINKING	C5 H9 N O4		--
DGN	B [auth D]	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DHI	B [auth D]	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DIL	B [auth D]	D-PEPTIDE LINKING	C6 H13 N O2		--
DLE	B [auth D]	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	B [auth D]	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DNE	B [auth D]	D-PEPTIDE LINKING	C6 H13 N O2		--
DPN	B [auth D]	D-PEPTIDE LINKING	C9 H11 N O2		--
DPR	B [auth D]	D-PEPTIDE LINKING	C5 H9 N O2		--
DSG	B [auth D]	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DSN	B [auth D]	D-PEPTIDE LINKING	C3 H7 N O3		--
DTH	B [auth D]	D-PEPTIDE LINKING	C4 H9 N O3		--
DTY	B [auth D]	D-PEPTIDE LINKING	C9 H11 N O3		--
DVA	B [auth D]	D-PEPTIDE LINKING	C5 H11 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.271 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.914	α = 81.91
b = 29.969	β = 72.38
c = 39.726	γ = 62.43

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references