3NCJ | pdb_00003ncj

Crystal structure of Fab15 Mut8

• PDB DOI: https://doi.org/10.2210/pdb3NCJ/pdb

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


• Deposited: 2010-06-04 Released: 2010-08-18 
• Deposition Author(s): Luo, J., Feng, Y., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.225 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Co-evolution of antibody stability and Vk CDR-L3 canonical structure

Luo, J., Feng, Y., Gilliland, G.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 48.22 kDa 
• Atom Count: 4,028 
• Modeled Residue Count: 439 
• Deposited Residue Count: 439 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab15 Mut8 light chain	A [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab15 Mut8 heavy chain	B [auth H]	225	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth L], D [auth L], G [auth H], H	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	E [auth L], I [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.225 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.55	α = 90
b = 74.7	β = 104.23
c = 65.39	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Luo, J., Feng, Y., Gilliland, G.L.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-03-31
  Changes: Derived calculations, Source and taxonomy
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary