MolNFT v1 · #154346 · protein
The open state of RGLG1 vwa domain
6K8B · E3 ubiquitin-protein ligase RGLG1: “The open state of RGLG1 vwa domain”. X-ray diffraction, 2 ligands (CA, MG), 6 pockets (best druggability 0.53). MolNFT v1 #154346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K8B
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RGLG1
- EC
- 2.3.2.27
- UniProt
- Q9SS90
- Ligands
- CA, MG
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase RGLG1 (EC 2.3.2.27) | protein | 280 | 38% helix, 15% strand | Q9SS90 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.53 | 0.80 | 30 | empty |
| 2 | 108 | 0.41 | 0.76 | 20 | empty |
| 3 | 108 | 0.38 | 0.75 | 28 | empty |
| 4 | 102 | 0.36 | 0.74 | 26 | empty |
| 5 | 63 | 0.29 | 0.74 | 17 | CA |
Interfaces
1 interface between chains.
- A–B · 804 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
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 Q9SS90
- Elsewhere: RCSB PDB 6K8B · PDBe 6K8B · UniProt Q9SS90
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