Crystal structure of a human Cdc34-ubiquitin thioester mimetic. Determined by X-ray diffraction at 1.5 Å resolution. Released 7 Aug 2019.
Explore 6NYO in 3D Show helices and sheets RCSB PDB PDBe
6NYO contains 16 α-helices and 14 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 8-22 | 15 | |
| α-helix | 24-25 | 2 | |
| β-strand | 28-32 | 5 | 1 |
| β-strand | 40-46 | 7 | 1 |
| α-helix | 47-48 | 2 | |
| β-strand | 57-63 | 7 | 1 |
| α-helix | 72-73 | 2 | |
| β-strand | 74-77 | 4 | 1 |
| β-strand | 86 | 1 | 2 |
| β-strand | 91 | 1 | 1 |
| β-strand | 92 | 1 | 2 |
| α-helix | 95-97 | 3 | |
| α-helix | 110-112 | 3 | |
| α-helix | 120-132 | 13 | |
| α-helix | 142-153 | 12 | |
| α-helix | 160-171 | 12 | |
| α-helix | 173-178 | 6 | |
| α-helix | 187-190 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 0-6 | 7 | 3 |
| β-strand | 12-18 | 7 | 3 |
| β-strand | 22 | 1 | 4 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 3 |
| β-strand | 48-49 | 2 | 3 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 4 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 3 |
| α-helix | 72-73 | 2 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ubiquitin-conjugating enzyme E2 R2 | A | protein | 204 | Homo sapiens | Q712K3 (AlphaFold model) |
| Ubiquitin | E | protein | 96 | Schizosaccharomyces pombe | P0CH08 (AlphaFold model) |
>6NYO_1 Ubiquitin-conjugating enzyme E2 R2 (chains A) GAMAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYF KAHIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVKISILHPPVDDPQSGELPSERWNPTQ NVRTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEK DGVKVPTTLAEYCIKTKVPSNDNS
>6NYO_2 Ubiquitin (chains E) MGSSHHHHHHSSGLVPRGSHMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
| ID | Name | Formula | Copies |
|---|---|---|---|
| U94 | 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinon… | C20 H21 Cl2 N O6 | 1 |
| PO4 | Phosphate ion | O4 P | 1 |
Water and common crystallization additives (EDO) are not listed.
Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Williams, K.M., Qie, S., Atkison, J.H. et al. Nat Commun (2019) 10:3296-3296. DOI 10.1038/s41467-019-11061-8 · PubMed
Other PDB entries of the same protein (UniProt Q712K3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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