Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair
Tu, C., Terraube, V., Tam, A., Stochaj, W., Fennell, B., Lin, L., Stahl, M., LaVallie, E., Somers, W., Finlay, W., Mosyak, L., Bard, J., Cunningham, O.To be published.
Experimental Data Snapshot
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84 | A [auth H], B [auth J] | 264 | Homo sapiens | Mutation(s): 0 Gene Names: IGHV1-69-2 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A0A0B4J2H0 (Homo sapiens) Explore A0A0B4J2H0 Go to UniProtKB: A0A0B4J2H0 | |||||
GTEx: ENSG00000280411 | |||||
Find proteins for P01704 (Homo sapiens) Explore P01704 Go to UniProtKB: P01704 | |||||
GTEx: ENSG00000211666 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | A0A0B4J2H0P01704 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 4 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PEG Query on PEG | RA [auth J], Z [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
SO4 Query on SO4 | CA [auth J], DA [auth J], EA [auth J], G [auth H], H | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
EDO Query on EDO | FA [auth J] GA [auth J] HA [auth J] I [auth H] IA [auth J] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
CL Query on CL | AA [auth J] BA [auth J] C [auth H] D [auth H] E [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 69.98 | α = 90 |
b = 80.36 | β = 90 |
c = 119.24 | γ = 90 |
Software Name | Purpose |
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BUSTER | refinement |
SCALA | data scaling |
MOLREP | phasing |