Research workbench
Cbs domain tandem of site-2 protease from archaeoglobus fulgidus in complex with llama nanobody - apo form
Analyse Cbs domain tandem of site-2 protease from archaeoglobus fulgidus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G5R
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Site-2 protease; Nanobody
- EC
- 3.4.24.85
- UniProt
- O29915
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-2 protease (EC 3.4.24.85) | protein | 122 | 34% helix, 26% strand | O29915 |
| B | Nanobody | protein | 120 | 5% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.49 | 0.85 | 15 | empty |
| 2 | 57 | 0.37 | 0.79 | 19 | SO4 |
| 3 | 79 | 0.35 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 790 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5G5R · CBS domain tandem of site-2 protease from Archaeoglobus fulgidus in complex with llama… · 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 O29915
- Elsewhere: RCSB PDB 5G5R · PDBe 5G5R · UniProt O29915
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.