Research workbench
Structure of an E1-E2-ubiquitin thioester mimetic
Analyse Structure of an E1-E2-ubiquitin thioester mimetic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K5J
- Type
- protein
- Length
- 9,613 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Ubiquitin-activating enzyme E1 1; Ubiquitin-conjugating enzyme E2-34 kda
- EC
- 6.2.1.45, 2.3.2.23
- UniProt
- P69326, P22515, P14682
- Ligands
- AMP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 23 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N, P | Ubiquitin | protein | 80 | 19% helix, 34% strand | P69326 |
| D | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 972 | 40% helix, 17% strand | P22515 |
| F | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 152 | 33% helix, 19% strand | P14682 |
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 971 | 40% helix, 18% strand | P22515 |
| B | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 153 | 32% helix, 19% strand | P14682 |
| C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 972 | 41% helix, 17% strand | P22515 |
| E | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 151 | 34% helix, 19% strand | P14682 |
| G | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 973 | 41% helix, 17% strand | P22515 |
| H | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 152 | 32% helix, 18% strand | P14682 |
| I | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 979 | 40% helix, 18% strand | P22515 |
| J | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 156 | 34% helix, 20% strand | P14682 |
| K | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 979 | 41% helix, 18% strand | P22515 |
| L | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 155 | 32% helix, 19% strand | P14682 |
| M | Ubiquitin | protein | 77 | 19% helix, 34% strand | P69326 |
| O | Ubiquitin | protein | 73 | 21% helix, 27% strand | P69326 |
| Q | Ubiquitin | protein | 76 | 20% helix, 33% strand | P69326 |
| R | Ubiquitin | protein | 76 | 20% helix, 34% strand | P69326 |
| S | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 971 | 41% helix, 17% strand | P22515 |
| T | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 153 | 32% helix, 18% strand | P14682 |
| U | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 973 | 40% helix, 18% strand | P22515 |
| V | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 146 | 36% helix, 18% strand | P14682 |
| W | Ubiquitin | protein | 70 | 26% helix, 30% strand | P69326 |
| X | Ubiquitin | protein | 73 | 21% helix, 33% strand | P69326 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 7 copies · chains D, A, C, G, I, K, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.82 | 0.83 | 109 | empty |
| 2 | 911 | 0.79 | 0.82 | 103 | empty |
| 3 | 961 | 0.79 | 0.81 | 74 | empty |
| 4 | 640 | 0.78 | 0.84 | 75 | empty |
| 5 | 707 | 0.78 | 0.82 | 66 | empty |
Interfaces
41 interfaces between chains.
- D–I · 1869 Ų buried · 14 hydrogen bonds · protein-protein
- A–K · 1798 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 1773 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 1703 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1545 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 isopeptide, 1 covalent (disulfide, isopeptide, covalent ligand).
Compared structures
- 7K5J · Structure of an E1-E2-ubiquitin thioester mimetic · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P69326
- Every structure of UniProt P22515
- Every structure of UniProt P14682
- Elsewhere: RCSB PDB 7K5J · PDBe 7K5J · UniProt P69326 · UniProt P22515 · UniProt P14682
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