6VRY | pdb_00006vry

Structure of NCI09 fab in complex with SIV V2 peptide

• PDB DOI: https://doi.org/10.2210/pdb6VRY/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Macaca mulatta, Simian immunodeficiency virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-02-10 Released: 2020-12-30 
• Deposition Author(s): Gorman, J., Ahmadi, M., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

HIV vaccine candidate with V1 deletion reveals virus vulnerability to V2 antibodies

Gorman, J., Ahmadi, M., Kwong, P.D.

(2020) iScience 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 51.37 kDa 
• Atom Count: 4,192 
• Modeled Residue Count: 450 
• Deposited Residue Count: 466 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NCI09 light chain	A [auth L]	214	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SIV V2 peptide	B [auth G]	16	Simian immunodeficiency virus	Mutation(s): 0
UniProt
Find proteins for P08810 (Simian immunodeficiency virus (isolate Mm251)) Explore P08810  Go to UniProtKB:  P08810

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NCI09 heavy chain	C [auth H]	236	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.76	α = 90
b = 72.087	β = 90
c = 100.833	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Gorman, J., Ahmadi, M., Kwong, P.D.

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary