Research workbench
Structure of the first RCC1-like domain of HERC2
Analyse Structure of the first RCC1-like domain of HERC2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L1M
- Type
- protein
- Length
- 1,067 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase HERC2
- EC
- 6.3.2.-
- UniProt
- O95714
- Ligands
- UNX, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase HERC2 (EC 6.3.2.-) | protein | 358 | 9% helix, 43% strand | O95714 |
| B | E3 ubiquitin-protein ligase HERC2 (EC 6.3.2.-) | protein | 357 | 8% helix, 43% strand | O95714 |
| C | E3 ubiquitin-protein ligase HERC2 (EC 6.3.2.-) | protein | 352 | 9% helix, 44% strand | O95714 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 34 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.76 | 0.85 | 37 | empty |
| 2 | 455 | 0.76 | 0.85 | 38 | UNX |
| 3 | 330 | 0.75 | 0.87 | 37 | UNX |
| 4 | 344 | 0.54 | 0.75 | 58 | SO4 |
| 5 | 333 | 0.52 | 0.74 | 56 | SO4, UNX |
Interfaces
3 interfaces between chains.
- A–C · 310 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 305 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 302 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4L1M · Structure of the first RCC1-like domain of HERC2 · the same entry in another collection · chain A against A, 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 O95714
- Elsewhere: RCSB PDB 4L1M · PDBe 4L1M · UniProt O95714
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