5YXK | pdb_00005yxk

High resolution crystal structure of Human B7-2 IgV domain in P21 space group

• PDB DOI: https://doi.org/10.2210/pdb5YXK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2017-12-05 Released: 2018-12-05 
• Deposition Author(s): Lankipalli, S., Ramagopal, U.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Comparitive structural analysis of human B7-2: New insights on its possible dimeric state

Lankipalli, S., Ramagopal, U.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.75 kDa 
• Atom Count: 3,730 
• Modeled Residue Count: 440 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-lymphocyte activation antigen CD86	A, B, C, D	111	Homo sapiens	Mutation(s): 0  Gene Names: CD86, CD28LG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P42081 (Homo sapiens) Explore P42081  Go to UniProtKB:  P42081
PHAROS:  P42081 GTEx:  ENSG00000114013

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.898	α = 90
b = 81.64	β = 90.32
c = 73.49	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Lankipalli, S., Ramagopal, U.A.

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary