8Z4C | pdb_00008z4c

The Fab fragment of anti-Fibrin monoclonal antibody 59D8

• PDB DOI: https://doi.org/10.2210/pdb8Z4C/pdb

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


• Deposited: 2024-04-17 Released: 2025-04-23 
• Deposition Author(s): Zhang, J., Sun, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.234 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the Fab fragment of monoclonal antibody targeting the knob B motif of fibrin

Zhang, J., Sun, C.

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)

Macromolecule Content 

• Total Structure Weight: 96.57 kDa 
• Atom Count: 6,966 
• Modeled Residue Count: 874 
• Deposited Residue Count: 884 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 59D8 heavy chain	A [auth H], C [auth A]	222	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 59D8 light chain	B [auth L], D	220	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.234 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.16	α = 90
b = 65.29	β = 97.9
c = 100.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Zhang, J., Sun, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release