Research workbench
Structure of an RSP5XUBXSNA3 complex: mechanism of ubiquitin ligation and lysine prioritization by a hect E3
Analyse Structure of an RSP5XUBXSNA3 complex: mechanism of ubiquitin ligation and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LCD
- Type
- protein
- Length
- 1,004 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RSP5; Protein SNA3; Ubiquitin
- EC
- 6.3.2.-
- UniProt
- P39940, P14359, P0CG48
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RSP5 (EC 6.3.2.-) | protein | 419 | 43% helix, 15% strand | P39940 |
| B | E3 ubiquitin-protein ligase RSP5 (EC 6.3.2.-) | protein | 413 | 45% helix, 16% strand | P39940 |
| C | Protein SNA3 | protein | 8 | 0% helix, 0% strand | P14359 |
| D | Protein SNA3 | protein | 14 | 43% helix, 0% strand | P14359 |
| E, F | Ubiquitin | protein | 75 | 16% helix, 27% strand | P0CG48 |
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.78 | 0.86 | 50 | empty |
| 2 | 462 | 0.77 | 0.85 | 50 | empty |
| 3 | 208 | 0.59 | 0.81 | 25 | empty |
| 4 | 183 | 0.55 | 0.80 | 25 | empty |
| 5 | 79 | 0.54 | 0.86 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–F · 718 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 663 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 421 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4LCD · Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine… · the same entry in another collection · chain F against F, TM-score 1.00
- P39940 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RSP5 (P39940) · a predicted model of the same protein · chain A against A, TM-score 0.67
- P14359 · AlphaFold monomer V2.0 prediction for protein SNA3 (P14359) · a predicted model of the same protein · chain C against A, TM-score 0.45
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 P39940
- Every structure of UniProt P14359
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4LCD · PDBe 4LCD · UniProt P39940 · UniProt P14359 · UniProt P0CG48
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