6V6W

Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.311 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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.Shapero, B.Lin, X.Ren, L.Zhang, L.Li, D.Zhou, Z.Feng, Y.Sou, C.Mann, C.J.Hao, Y.Sarkar, A.Hou, 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, Y.

(2020) Sci Adv 6: eabb1328


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
35O22 Fab Heavy chainG [auth A], A [auth D]243Human immunodeficiency virus 1Mutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
35O22 Fab Light chainH [auth B], B [auth E]216Human immunodeficiency virus 1Mutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120I [auth C], C [auth G]485Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
B11 DSS Fab heavy chainJ [auth F], D [auth I]235Human immunodeficiency virus 1Mutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
B11 Fab light chainK [auth H], E [auth J]215Human immunodeficiency virus 1Mutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41L [auth K], F [auth T]140Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S9 (Human immunodeficiency virus 1)
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Oligosaccharides

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Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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 L], P [auth O]4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth M], Q [auth P]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseO [auth N], R [auth Q]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 1 Unique
IDChainsName / 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] , EA [auth C] , FA [auth C] , GA [auth C] , HA [auth C] , 
AA [auth G],  BA [auth T],  CA [auth T],  DA [auth T],  EA [auth C],  FA [auth C],  GA [auth C],  HA [auth C],  IA [auth C],  JA [auth C],  KA [auth C],  LA [auth C],  MA [auth C],  NA [auth K],  OA [auth K],  PA [auth K],  S [auth G],  T [auth G],  U [auth G],  V [auth G],  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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.311 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.534α = 90
b = 148.534β = 90
c = 843.554γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data scaling
HKL-2000data processing
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Derived calculations