4KKN | pdb_00004kkn

Crystal structure of bovine CTLA-4, PSI-NYSGRC-012704

PDB DOI: https://doi.org/10.2210/pdb4KKN/pdb

Deposited: 2013-05-06 Released: 2013-06-12
Deposition Author(s): Kumar, P.R., Ahmed, M., Banu, R., Bhosle, R., Bonanno, J., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S.J., Scott Glenn, A., Hammonds, J., Hillerich, B., Khafizov, K., Lafleur, J., Attonito, J., Love, J.D., Patel, H., Patel, R., Seidel, R.D., Smith, B., Stead, M., Toro, R., Casadevall, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of bovine CTLA-4, PSI-NYSGRC-012704

Kumar, P.R., Casadevall, A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 15.19 kDa
Atom Count: 969
Modeled Residue Count: 117
Deposited Residue Count: 133
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte associated protein 4	A	133	Bos taurus	Mutation(s): 0 Gene Names: CTLA-4, CTLA4
UniProt
Find proteins for Q28090 (Bos taurus) Explore Q28090 Go to UniProtKB: Q28090
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q28090
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.241 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.875	α = 90
b = 87.831	β = 90
c = 52.25	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Atoms-to-Animals: The Immune Function Network (IFN)

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary