MolNFT v1 · #119760 · protein
Cbs domain tandem of site-2 protease from archaeoglobus fulgidus in complex with llama nanobody - nucleotide-bound form
5G5X: “Cbs domain tandem of site-2 protease from archaeoglobus fulgidus in complex with llama nanobody…”. X-ray diffraction, 2 ligands (AMP, ATP), 3 pockets (best druggability 0.40). MolNFT v1 #119760 on GenesisL1: 3D structure, binding…
- PDB
- 5G5X
- Type
- protein
- Length
- 237 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
- AMP, ATP
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-2 protease (EC 3.4.24.85) | protein | 119 | 30% helix, 26% strand | O29915 |
| B | Nanobody | protein | 118 | 5% helix, 52% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
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 | 0.40 | 0.80 | 15 | AMP |
| 2 | 74 | 0.36 | 0.77 | 18 | empty |
| 3 | 62 | 0.31 | 0.75 | 15 | ATP |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5G5X · 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 5G5X · PDBe 5G5X · UniProt O29915
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