Research workbench
Crystal structure of the third RCC1-like domain of HERC1
Analyse Crystal structure of the third RCC1-like domain of HERC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O2W
- Type
- protein
- Length
- 1,459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase HERC1
- EC
- 6.3.2.-
- UniProt
- Q15751
- Ligands
- MG, UNX, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | E3 ubiquitin-protein ligase HERC1 (EC 6.3.2.-) | protein | 365 | 12% helix, 43% strand | Q15751 |
| D | E3 ubiquitin-protein ligase HERC1 (EC 6.3.2.-) | protein | 364 | 11% helix, 43% strand | Q15751 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
- UNX · Unknown atom or ion · ion · 25 copies · chains A, D, B, C
- CL · Chloride ion · ion · 5 copies · chains A, D
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 | 989 | 0.77 | 0.79 | 96 | CL, UNX |
| 2 | 413 | 0.75 | 0.84 | 40 | UNX |
| 3 | 428 | 0.75 | 0.84 | 41 | empty |
| 4 | 452 | 0.74 | 0.84 | 41 | UNX |
| 5 | 483 | 0.74 | 0.83 | 46 | empty |
Interfaces
5 interfaces between chains.
- B–D · 486 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 460 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 451 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 130 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4O2W · Crystal structure of the third RCC1-like domain of HERC1 · 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 Q15751
- Elsewhere: RCSB PDB 4O2W · PDBe 4O2W · UniProt Q15751
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