5E5M | pdb_00005e5m

Crystal structure of mouse CTLA-4 in complex with nanobody

PDB DOI: https://doi.org/10.2210/pdb5E5M/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Camelidae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-10-08 Released: 2016-10-12
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.247 (Depositor), 0.249 (DCC)
R-Value Work:
0.193 (Depositor), 0.197 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of mouse CTLA-4 in complex with nanobody

Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 106.54 kDa
Atom Count: 6,966
Modeled Residue Count: 906
Deposited Residue Count: 984
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte protein 4	A, C, E, G	117	Mus musculus	Mutation(s): 0 Gene Names: Ctla4, Cd152
UniProt
Find proteins for P09793 (Mus musculus) Explore P09793 Go to UniProtKB: P09793
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09793
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CTLA-4 nanobody	B, D, F, H	129	Camelidae	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.247 (Depositor), 0.249 (DCC)
R-Value Work: 0.193 (Depositor), 0.197 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.22	α = 90
b = 111.572	β = 90
c = 112.881	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-10-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-12
Type: Initial release
Version 1.1: 2019-01-30
Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2024-11-20
Changes: Data collection, Database references, 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.