6N35

Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

• PDB DOI: https://doi.org/10.2210/pdb6N35/pdb
• Entry: 6N35 supersedes: 1OP3

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


• Deposited: 2018-11-14 Released: 2018-11-28 
• Deposition Author(s): Calarese, D.A., Stanfield, R.L., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 94.92 kDa 
• Atom Count: 7,150 
• Modelled Residue Count: 860 
• Deposited Residue Count: 874 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2G12 light chain	A [auth L], C [auth K]	213	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX7 (Homo sapiens) Explore P0DOX7  Go to UniProtKB:  P0DOX7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2G12 heavy chain	B [auth H], D [auth M]	224	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	E [auth A]	2		N/A
Glycosylation Resources
GlyTouCan:  G53402KW GlyCosmos:  G53402KW GlyGen:  G53402KW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	H [auth M]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BEZ	F [auth L]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
GOL	G [auth K]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	E [auth A]	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.725	α = 90
b = 94.034	β = 90
c = 169.187	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Currently 6N35 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Calarese, D.A., Stanfield, R.L., Wilson, I.A.
• This entry supersedes: 1OP3

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM46192

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary