8GSI

Structure of the cobolimab Fab

• PDB DOI: https://doi.org/10.2210/pdb8GSI/pdb

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


• Deposited: 2022-09-06 Released: 2023-09-06 
• Deposition Author(s): Heo, Y.S., Choi, S.B.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of the Fab fragment of cobolimab, an investigational antibody targeting Tim-3 for immune-oncology.

Heo, Y.S., Choi, S.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.66 kDa 
• Atom Count: 4,403 
• Modelled Residue Count: 546 
• Deposited Residue Count: 569 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain	A	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain	B	225	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	C [auth F]	130	Camelus bactrianus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.3	α = 90
b = 119.3	β = 90
c = 184.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Heo, Y.S., Choi, S.B.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary