5E6V

Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit

• PDB DOI: https://doi.org/10.2210/pdb5E6V/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-10-10 Released: 2016-03-02 
• Deposition Author(s): Sen, M., Springer, T.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1YUK

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: 25.97 kDa 
• Atom Count: 2,027 
• Modelled Residue Count: 224 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-2	A	224	Homo sapiens	Mutation(s): 0  Gene Names: ITGB2, CD18, MFI7
UniProt & NIH Common Fund Data Resources
Find proteins for P05107 (Homo sapiens) Explore P05107  Go to UniProtKB:  P05107
PHAROS:  P05107 GTEx:  ENSG00000160255

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28454KX GlyCosmos:  G28454KX GlyGen:  G28454KX

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.6	α = 90
b = 31.818	β = 91.2
c = 74.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SOLVE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Sen, M., Springer, T.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	NCI CA031798

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-16
  Changes: Database references
• Version 1.2: 2016-05-11
  Changes: Database references
• Version 1.3: 2017-03-15
  Changes: Experimental preparation, Other
• Version 1.4: 2017-09-27
  Changes: Author supporting evidence
• Version 2.0: 2019-12-04
  Changes: Author supporting evidence, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary