6XY2

Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody

PDB DOI: https://doi.org/10.2210/pdb6XY2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-01-29 Released: 2020-12-09
Deposition Author(s): Gao, H., Zhou, A.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.292
R-Value Work: 0.249
R-Value Observed: 0.251

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of CTLA-4 complexed with a pH-sensitive cancer immunotherapeutic antibody.

Gao, H., Cai, H., Liu, J., Wang, X., Zheng, P., Devenport, M., Xu, T., Dou, F., Liu, Y., Zhou, A.

(2020) Cell Discov 6: 79-79

PubMed: 33298884 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-020-00202-9
Primary Citation of Related Structures:
6XY2

Organizational Affiliation

State Key Laboratory of Cognitive Neuroscience and Learning, and Beijing Key Laboratory of Genetic Engineering Drugs and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.

Macromolecule Content

Total Structure Weight: 63.5 kDa
Atom Count: 4,163
Modelled Residue Count: 553
Deposited Residue Count: 584
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte protein 4	A	123	Homo sapiens	Mutation(s): 0 Gene Names: CTLA4, CD152
UniProt & NIH Common Fund Data Resources
Find proteins for P16410 (Homo sapiens) Explore P16410 Go to UniProtKB: P16410
PHAROS: P16410 GTEx: ENSG00000163599
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16410
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain	B [auth H]	247	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.292
R-Value Work: 0.249
R-Value Observed: 0.251
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.862	α = 90
b = 254.478	β = 90
c = 66.935	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Gao, H.

Zhou, A.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2020-12-23
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description