Research workbench
Crystal structure of RNF168 UDM1 in complex with LYS63-linked diubiquitin, form II
Analyse Crystal structure of RNF168 UDM1 in complex with LYS63-linked diubiquitin, form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XIT
- Type
- protein
- Length
- 450 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-40S ribosomal protein S27A; E3 ubiquitin-protein ligase RNF168
- EC
- 2.3.2.27
- UniProt
- P62983, Q8IYW5
- Ligands
- PR
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | Ubiquitin-40S ribosomal protein S27A | protein | 76 | 20% helix, 34% strand | P62983 |
| E | E3 ubiquitin-protein ligase RNF168 (EC 2.3.2.27) | protein | 75 | 92% helix, 0% strand | Q8IYW5 |
| H | Ubiquitin-40S ribosomal protein S27A | protein | 74 | 20% helix, 35% strand | P62983 |
| A | E3 ubiquitin-protein ligase RNF168 (EC 2.3.2.27) | protein | 76 | 96% helix, 0% strand | Q8IYW5 |
| B | Ubiquitin-40S ribosomal protein S27A | protein | 73 | 21% helix, 36% strand | P62983 |
Ligands and binding sites
- PR · Praseodymium ion · metal · 3 copies · chains E
- GOL · Glycerol · additive · 5 copies · chains D, A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.47 | 0.76 | 28 | empty |
| 2 | 129 | 0.44 | 0.76 | 18 | empty |
| 3 | 91 | 0.43 | 0.78 | 14 | empty |
| 4 | 97 | 0.36 | 0.74 | 17 | empty |
| 5 | 84 | 0.34 | 0.75 | 12 | empty |
Interfaces
9 interfaces between chains.
- A–B · 616 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 606 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 569 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 553 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 125 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 5XIT · Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II · the same entry in another collection · chain F against F, TM-score 1.00
- P62983 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62983) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q8IYW5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF168 (Q8IYW5) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P62983
- Every structure of UniProt Q8IYW5
- Elsewhere: RCSB PDB 5XIT · PDBe 5XIT · UniProt P62983 · UniProt Q8IYW5
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