Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3
Lange, S.M., Kulathu, Y.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Polyubiquitin-B | 72 | Homo sapiens | Mutation(s): 0  Gene Names: UBB | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47 | |||||
PHAROS:  P0CG47 GTEx:  ENSG00000170315  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0CG47 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Polyubiquitin-B | 76 | Homo sapiens | Mutation(s): 2  Gene Names: UBB | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47 | |||||
PHAROS:  P0CG47 GTEx:  ENSG00000170315  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0CG47 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Synthetic nanobody NbSL3 | 129 | synthetic construct | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Ligands 4 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GOL Query on GOL | K [auth B], S [auth F] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CL Query on CL | L [auth C] O [auth D] R [auth E] T [auth F] V [auth G] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
MG Query on MG | I [auth A] J [auth A] N [auth C] P [auth D] Q [auth E] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
NA Query on NA | M [auth C], Y [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 54.389 | α = 90 |
b = 97.615 | β = 109.959 |
c = 74.967 | γ = 90 |
Software Name | Purpose |
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PHENIX | refinement |
XDS | data reduction |
MxCuBE | data collection |
XDS | data scaling |
PHASER | phasing |
Funding Organization | Location | Grant Number |
---|---|---|
Medical Research Council (MRC, United Kingdom) | United Kingdom | MC_UU_00018/3 |
European Molecular Biology Organization (EMBO) | United Kingdom | Young Investigator Programme |