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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.248 (Depositor), 0.263 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5YXK

This is version 1.2 of the entry. See complete history.

Literature

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

Lankipalli, S., Ramagopal, U.A.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42081
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248 (Depositor), 0.263 (DCC)
R-Value Work: 0.199 (Depositor)
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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-12-05

Deposition Author(s):

Ramagopal, U.A.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.