9UCG | pdb_00009ucg

A Fab structure with a covalent bond

• PDB DOI: https://doi.org/10.2210/pdb9UCG/pdb

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


• Deposited: 2025-04-04 Released: 2026-04-08 
• Deposition Author(s): Makabe, K., Nakanishi, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.281 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: in silico

Literature

Structure of Fab fragment

Makabe, K., Nakanishi, T., Tachibana, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95.74 kDa 
• Atom Count: 6,636 
• Modeled Residue Count: 857 
• Deposited Residue Count: 880 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-CD63 VH-CH1 iso	A, C	222	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-CD63 VL-CL iso	B, D	218	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.281 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.233	α = 90
b = 101.233	β = 90
c = 212.417	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-08 
Deposition Author(s): Makabe, K., Nakanishi, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2026-04-08
  Type: Initial release