6UTK | pdb_00006utk

Crystal structure of 438-B11 Fab in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22 at 3.80 Angstrom

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.317 (Depositor), 0.319 (DCC) 
  • R-Value Work: 
    0.299 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 
    0.300 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6UTK

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 

Literature

A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite

Kumar, S., Ju, B., Shapiro, B., Lin, X., Ren, L., Zhang, L., Li, D., Zhou, Z., Feng, Y., Sou, C., Mann, C.J., Hao, Y., Sarkar, A., Jou, J., Nunnally, C., Hong, K., Wang, S., Ge, X., Su, B., Landais, E., Sok, D., Zwick, M.B., He, L., Zhu, J., Wilson, I.A., Shao, Z.

(2020) Sci Adv 6: eabb1328

Macromolecule Content 

  • Total Structure Weight: 181.89 kDa 
  • Atom Count: 12,419 
  • Modeled Residue Count: 1,484 
  • Deposited Residue Count: 1,530 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
35O22 Fab Heavy ChainA [auth D]243Homo sapiensMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
35O22 Fab Light ChainB [auth E]216Homo sapiensMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
B11 Fab Light ChainC [auth L]213Homo sapiensMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120D [auth G]485Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 18
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41E [auth T]140Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S9 (Human immunodeficiency virus type 1)
Explore Q2N0S9 
Go to UniProtKB:  Q2N0S9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S9
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
B11 Fab Heavy chainF [auth H]233Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth A],
K [auth I],
Q [auth P],
R [auth Q],
U		3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth B]10N-Glycosylation
Glycosylation Resources
GlyTouCan: G15494PG
GlyCosmos: G15494PG
GlyGen: G15494PG
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth C],
J [auth F],
P [auth O]		2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth J],
N [auth M]		4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth K]11N-Glycosylation
Glycosylation Resources
GlyTouCan: G60230HH
GlyCosmos: G60230HH
GlyGen: G60230HH
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseO [auth N]6N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC
GlyCosmos: G09724ZC
GlyGen: G09724ZC
Entity ID: 13
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseS [auth R]7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL
Entity ID: 14
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseT [auth S]5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 15
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
V
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G79924RM
GlyCosmos: G79924RM
GlyGen: G79924RM

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG


Download:Ideal Coordinates CCD File
AA [auth G]
BA [auth T]
CA [auth T]
DA [auth T]
W [auth G]
AA [auth G],
BA [auth T],
CA [auth T],
DA [auth T],
W [auth G],
X [auth G],
Y [auth G],
Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.317 (Depositor), 0.319 (DCC) 
  • R-Value Work:  0.299 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 0.300 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.308α = 90
b = 247.308β = 90
c = 257.612γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 2.0: 2020-10-07
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-11-20
    Changes: Structure summary