MolNFT v1 · #140121 · protein
Crystal structure of bacillus subtilis tmcal bound with ATP (semet derivative)
5Y0N · UPF0348 protein B4417_3650: “Crystal structure of bacillus subtilis tmcal bound with ATP (semet derivative)”. X-ray diffraction, 1 ligand (ATP), 10 pockets (best druggability 0.75). MolNFT v1 #140121 on GenesisL1: 3D structure…
- PDB
- 5Y0N
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0348 protein B4417_3650
- UniProt
- A0A164SIT4
- Ligands
- ATP
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | UPF0348 protein B4417_3650 | protein | 401 | 53% helix, 10% strand | A0A164SIT4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.75 | 0.85 | 36 | ATP |
| 2 | 401 | 0.72 | 0.83 | 44 | ATP |
| 3 | 642 | 0.69 | 0.77 | 75 | empty |
| 4 | 54 | 0.43 | 0.83 | 12 | empty |
| 5 | 126 | 0.38 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1145 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5Y0N · Crystal structure of Bacillus subtilis TmcAL bound with ATP (SeMet derivative) · 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 A0A164SIT4
- Elsewhere: RCSB PDB 5Y0N · PDBe 5Y0N · UniProt A0A164SIT4
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