6RPJ | pdb_00006rpj

A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4

• PDB DOI: https://doi.org/10.2210/pdb6RPJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Camelus bactrianus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-05-14 Released: 2020-07-08 
• Deposition Author(s): Gao, H., Zhou, A., Zhang, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Literature

A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4

Gao, H., Zhou, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118.42 kDa 
• Atom Count: 7,424 
• Modeled Residue Count: 973 
• Deposited Residue Count: 1,084 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte protein 4	A, C, E, G	129	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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P16410-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A non-blocking CTLA-4 nanobody	B, D, F, H	142	Camelus bactrianus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J, K	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth C], M [auth C], N [auth E], P [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	O [auth E], Q [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 309.977	α = 90
b = 75.708	β = 100.05
c = 83.047	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Gao, H., Zhou, A., Zhang, F.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 3.0: 2020-11-11
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary