3CMO | pdb_00003cmo

HIV neutralizing monoclonal antibody YZ18

• PDB DOI: https://doi.org/10.2210/pdb3CMO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2008-03-24 Released: 2008-08-05 
• Deposition Author(s): Jin, L., Prasad, V., Paul, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.247 (DCC) 

Starting Model: experimental

Literature

HIV neutralizing monoclonal antibody YZ18

Jin, L., Prasad, V., Paul, S.

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)

Biological Assembly 2  

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 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.41 kDa 
• Atom Count: 6,720 
• Modeled Residue Count: 863 
• Deposited Residue Count: 864 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	A [auth L], C [auth X]	210	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	B [auth H], D [auth Y]	222	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q6PJA7 (Mus musculus) Explore Q6PJA7  Go to UniProtKB:  Q6PJA7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.247 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.65	α = 90
b = 69.94	β = 94.93
c = 84.36	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Jin, L., Prasad, V., Paul, S.

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary