5UBZ | pdb_00005ubz

Fab structure of HIV gp120 specific mAb 1E12

• PDB DOI: https://doi.org/10.2210/pdb5UBZ/pdb

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


• Deposited: 2016-12-21 Released: 2018-01-10 
• Deposition Author(s): Pan, R., Kong, X.-P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.264 (Depositor) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

High Antibody Diversity and Low Inter-clonal Competition Favor Production of Functional Neutralizing Antibodies

Smith, S.A., Burton, S.L., Spicer, L., Pan, R., Kilembe, W., Lakhi, S., Karita, E., Price, M., Allen, S., Hunter, E., Kong, X.-P., Derdeyn, C.A.

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)

Macromolecule Content 

• Total Structure Weight: 46.75 kDa 
• Atom Count: 3,263 
• Modeled Residue Count: 435 
• Deposited Residue Count: 441 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-HIV1 gp120 mAb 1E12 Fab heavy chain	A [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-HIV1 gp120 mAb 1E12 Fab light chain	B [auth L]	213	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.264 (Depositor) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.174	α = 90
b = 79.174	β = 90
c = 124.377	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	model building
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Pan, R., Kong, X.-P.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI58706
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI100151

Revision History  

• Version 1.0: 2018-01-10
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary