Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound). Determined by X-ray diffraction at 1.43 Å resolution. Released 9 Aug 2017.
Explore 5KYC in 3D Show helices and sheets RCSB PDB PDBe
5KYC contains 23 α-helices and 28 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 |
|---|---|---|---|
| β-strand | 216 | 1 | 1 |
| α-helix | 225-233 | 9 | |
| α-helix | 236-243 | 8 | |
| α-helix | 256-269 | 14 | |
| α-helix | 273 | 1 | |
| β-strand | 274 | 1 | 1 |
| α-helix | 275 | 1 | |
| α-helix | 277-283 | 7 | |
| α-helix | 288-293 | 6 | |
| α-helix | 296-311 | 16 | |
| α-helix | 319-324 | 6 | |
| β-strand | 326-334 | 9 | 2 |
| β-strand | 340-347 | 8 | 2 |
| β-strand | 350-353 | 4 | 3 |
| β-strand | 359 | 1 | 4 |
| α-helix | 360-367 | 8 | |
| β-strand | 371-373 | 3 | 2 |
| α-helix | 375-377 | 3 | |
| β-strand | 379-380 | 2 | 5 |
| α-helix | 382-384 | 3 | |
| β-strand | 386-387 | 2 | 5 |
| β-strand | 389-395 | 7 | 2 |
| β-strand | 401-407 | 7 | 3 |
| β-strand | 409-412 | 4 | 6 |
| β-strand | 417-420 | 4 | 6 |
| β-strand | 426 | 1 | 4 |
| β-strand | 430-432 | 3 | 3 |
| α-helix | 434-436 | 3 | |
| β-strand | 437 | 1 | 2 |
| β-strand | 447-457 | 11 | 3 |
| β-strand | 464-469 | 6 | 3 |
| β-strand | 478-481 | 4 | 3 |
| β-strand | 484-487 | 4 | 3 |
| α-helix | 490-493 | 4 | |
| α-helix | 495-497 | 3 | |
| α-helix | 507-510 | 4 | |
| β-strand | 511-520 | 10 | 3 |
| α-helix | 521-523 | 3 | |
| α-helix | 524-527 | 4 | |
| α-helix | 533-535 | 3 | |
| α-helix | 538-547 | 10 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-6 | 5 | 7 |
| β-strand | 12-16 | 5 | 7 |
| β-strand | 22 | 1 | 8 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 43-45 | 3 | 7 |
| β-strand | 48-49 | 2 | 7 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 8 |
| β-strand | 66-69 | 4 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ubiquitin carboxyl-terminal hydrolase 7 | B | protein | 351 | Homo sapiens | Q93009 (AlphaFold model) |
| Polyubiquitin-B | C | protein | 76 | Homo sapiens | P0CG47 (AlphaFold model) |
>5KYC_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains B) GSHMKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRV FYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRKLLDNVENKMKGTCVEGTIPKL FRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGE HGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPK DPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDD DLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK
>5KYC_2 Polyubiquitin-B (chains C) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG
| ID | Name | Formula | Copies |
|---|---|---|---|
| MLA | Malonic acid | C3 H4 O4 | 1 |
Water and common crystallization additives (GOL) are not listed.
Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation. Ozen, A., Rouge, L., Bashore, C. et al. Structure (2018) 26:72-84.e7. DOI 10.1016/j.str.2017.11.010 · PubMed
Other PDB entries of the same protein (UniProt Q93009 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 5KYC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.