8CWJ

Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies

Langley, D.B.Christ, D.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of CR3022 antibody FabA [auth H],
D [auth A]
230Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of CR3022 antibody FabB [auth L],
E [auth B]
220Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinC [auth G],
F [auth I]
204Pangolin coronavirusMutation(s): 0 
UniProt
Find proteins for A0A7D6PMV8 (Pangolin coronavirus)
Explore A0A7D6PMV8 
Go to UniProtKB:  A0A7D6PMV8
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UniProt GroupA0A7D6PMV8
Glycosylation
Glycosylation Sites: 2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of 4C12-B12 antibody FabG [auth J],
I [auth U]
230Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of 4C12-B12 antibody FabH [auth K],
J [auth V]
215Homo sapiensMutation(s): 0 
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Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth C],
L [auth D],
M [auth E]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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P [auth G]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

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DA [auth J]
EA [auth J]
GA [auth K]
IA [auth U]
KA [auth V]
DA [auth J],
EA [auth J],
GA [auth K],
IA [auth U],
KA [auth V],
LA [auth V],
MA [auth V],
N [auth H],
O [auth G],
Q [auth G],
U [auth I],
V [auth I],
W [auth I],
X [auth I],
Y [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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AA [auth I]
BA [auth I]
CA [auth I]
FA [auth J]
HA [auth K]
AA [auth I],
BA [auth I],
CA [auth I],
FA [auth J],
HA [auth K],
JA [auth U],
R [auth G],
S [auth G],
T [auth G],
Z [auth I]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.433α = 90
b = 144.097β = 117.51
c = 168.842γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description