Research workbench
Crystal structure of RNF168 UDM1 in complex with LYS63-linked diubiquitin, tetrameric form
Analyse Crystal structure of RNF168 UDM1 in complex with LYS63-linked diubiquitin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YDK
- Type
- protein
- Length
- 923 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF168; Ubiquitin-40S ribosomal protein S27A
- EC
- 2.3.2.27
- UniProt
- Q8IYW5, P62979
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF168 (EC 2.3.2.27) | protein | 81 | 95% helix, 0% strand | Q8IYW5 |
| B, H, E, K | Ubiquitin-40S ribosomal protein S27A | protein | 76 | 20% helix, 33% strand | P62979 |
| D | Ubiquitin-40S ribosomal protein S27A | protein | 75 | 20% helix, 32% strand | P62979 |
| G | E3 ubiquitin-protein ligase RNF168 (EC 2.3.2.27) | protein | 80 | 95% helix, 0% strand | Q8IYW5 |
| J, C, I | Ubiquitin-40S ribosomal protein S27A | protein | 73 | 21% helix, 36% strand | P62979 |
| F, L | E3 ubiquitin-protein ligase RNF168 (EC 2.3.2.27) | protein | 82 | 89% helix, 0% strand | Q8IYW5 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains J, L, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.75 | 0.80 | 93 | GOL |
| 2 | 700 | 0.72 | 0.78 | 64 | empty |
| 3 | 216 | 0.64 | 0.83 | 38 | GOL |
| 4 | 276 | 0.51 | 0.74 | 34 | empty |
| 5 | 129 | 0.42 | 0.76 | 26 | empty |
Interfaces
24 interfaces between chains.
- F–C · 673 Ų buried · 9 hydrogen bonds · protein-protein
- L–I · 670 Ų buried · 5 hydrogen bonds · protein-protein
- G–J · 667 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 660 Ų buried · 7 hydrogen bonds · protein-protein
- B–L · 590 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 5YDK · Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form · the same entry in another collection · chain I against I, 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 Q8IYW5
- Every structure of UniProt P62979
- Elsewhere: RCSB PDB 5YDK · PDBe 5YDK · UniProt Q8IYW5 · UniProt P62979
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