6DJ9: USP15 DUSP domain
Structure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV). Determined by X-ray diffraction at 3.1 Å resolution. Released 23 Jan 2019.
- Method
- X-ray diffraction
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 9,759
- Mol. weight
- 153 kDa
- Released
- 23 Jan 2019
Explore 6DJ9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6DJ9 contains 54 α-helices and 71 β-strands across 12 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.
Chain A: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-19 | 11 | |
| α-helix | 22-24 | 3 | |
| β-strand | 29-34 | 6 | 1 |
| α-helix | 35-45 | 11 | |
| β-strand | 71 | 1 | 2 |
| β-strand | 79 | 1 | 2 |
| α-helix | 80 | 1 | |
| β-strand | 85 | 1 | 1 |
| β-strand | 89-92 | 4 | 1 |
| α-helix | 94-101 | 8 | |
| α-helix | 106-107 | 2 | |
| β-strand | 114-116 | 3 | 1 |
| β-strand | 121 | 1 | 3 |
Chain B: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-20 | 12 | |
| β-strand | 30-34 | 5 | 4 |
| α-helix | 35-45 | 11 | |
| α-helix | 52-54 | 3 | |
| β-strand | 85 | 1 | 4 |
| β-strand | 89-93 | 5 | 4 |
| α-helix | 94-104 | 11 | |
| β-strand | 114 | 1 | 4 |
| β-strand | 121 | 1 | 5 |
| α-helix | 128-130 | 3 | |
Chain C: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-20 | 11 | |
| β-strand | 29-34 | 6 | 6 |
| α-helix | 35-45 | 11 | |
| β-strand | 85 | 1 | 6 |
| β-strand | 89-92 | 4 | 6 |
| α-helix | 94-103 | 10 | |
| β-strand | 114-116 | 3 | 6 |
| β-strand | 120-121 | 2 | 7 |
Chain D: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-20 | 12 | |
| β-strand | 29-33 | 5 | 8 |
| α-helix | 35-45 | 11 | |
| α-helix | 58-60 | 3 | |
| β-strand | 65 | 1 | 9 |
| β-strand | 85 | 1 | 10 |
| β-strand | 89 | 1 | 10 |
| β-strand | 90-92 | 3 | 8 |
| α-helix | 94-101 | 8 | |
| β-strand | 106 | 1 | 9 |
| β-strand | 114-116 | 3 | 8 |
| β-strand | 121 | 1 | 3 |
Chain E: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-16 | 7 | |
| β-strand | 30-34 | 5 | 11 |
| α-helix | 35-45 | 11 | |
| α-helix | 52-54 | 3 | |
| β-strand | 65 | 1 | 12 |
| β-strand | 85 | 1 | 11 |
| β-strand | 89-93 | 5 | 11 |
| α-helix | 94-101 | 8 | |
| α-helix | 105 | 1 | |
| β-strand | 106 | 1 | 12 |
| α-helix | 107 | 1 | |
| β-strand | 114-115 | 2 | 11 |
| β-strand | 121-122 | 2 | 7 |
Chain F: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-18 | 10 | |
| β-strand | 30-34 | 5 | 13 |
| α-helix | 35-45 | 11 | |
| α-helix | 52-54 | 3 | |
| α-helix | 58-60 | 3 | |
| β-strand | 65 | 1 | 14 |
| α-helix | 67-69 | 3 | |
| β-strand | 71 | 1 | 15 |
| β-strand | 79 | 1 | 15 |
| β-strand | 85 | 1 | 13 |
| β-strand | 89-93 | 5 | 13 |
| α-helix | 94-104 | 11 | |
| β-strand | 106 | 1 | 14 |
| β-strand | 115 | 1 | 13 |
| β-strand | 121 | 1 | 5 |
Chain G: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 16 |
| α-helix | 8-11 | 4 | |
| β-strand | 14-17 | 4 | 17 |
| α-helix | 25-28 | 4 | |
| α-helix | 31-35 | 5 | |
| β-strand | 43-46 | 4 | 17 |
| β-strand | 51 | 1 | 17 |
| β-strand | 70-73 | 4 | 17 |
Chain H: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24 | 1 | 18 |
| α-helix | 25-28 | 4 | |
| α-helix | 31-35 | 5 | |
| α-helix | 40-42 | 3 | |
| β-strand | 43-46 | 4 | 19 |
| β-strand | 51 | 1 | 19 |
| α-helix | 52-53 | 2 | |
| β-strand | 57 | 1 | 18 |
| α-helix | 59-61 | 3 | |
| α-helix | 69 | 1 | |
| β-strand | 70-73 | 4 | 19 |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin carboxyl-terminal hydrolase 15 | A, B, C, D, E, F | protein | 141 | Homo sapiens | Q9Y4E8 (AlphaFold model) |
| Ubiquitin Variant UbV 15.D | G, H, I, J, K, L | protein | 86 | Homo sapiens | |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>6DJ9_1 Ubiquitin carboxyl-terminal hydrolase 15 (chains A, B, C, D, E, F)
GAAAMAEGGAADLDTQRSDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMG
DQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARK
VVEQGMFVKHCKVEVYLTSSG
Sequence of entity 2 (G, H, I, J, K, L), FASTA
>6DJ9_2 Ubiquitin Variant UbV 15.D (chains G, H, I, J, K, L)
GAGMQIFVSTAWFCGKLITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESGLQLHRRLRPTSGSSG
Primary citation
Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Teyra, J., Singer, A.U., Schmitges, F.W. et al. Structure (2019) 27:590. DOI 10.1016/j.str.2019.01.002 · PubMed
Other PDB entries of the same protein (UniProt Q9Y4E8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4A3P 1.4 Å, Structure of USP15 DUSP-UBL deletion mutant
- 3T9L 1.5 Å, Structure of N-terminal DUSP-UBL domains of human USP15
- 6ML1 1.9 Å, Structure of the USP15 deubiquitinase domain in complex with an affinity-matured…
- 6GHA 1.98 Å, USP15 catalytic domain structure
- 7R2G 1.98 Å, USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2)
- 6CPM 2.01 Å, Structure of the USP15 deubiquitinase domain in complex with a third-generation…
- 6GH9 2.09 Å, USP15 catalytic domain in complex with small molecule
- 3LMN 2.15 Å, Oligomeric structure of the DUSP domain of human USP15
- 4A3O 2.2 Å, Crystal structure of the USP15 DUSP-UBL monomer
- 9VVV 2.3 Å, Crystal structure of USP15 catalytic domain in complex with Ub-PA
- 3PPA 2.35 Å, Structure of the Dusp-Ubl domains of Usp15
- 6CRN 2.5 Å, Structure of the USP15 deubiquitinase domain in complex with a high-affinity…
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