MolNFT v1 · #114406 · protein
Bacillus megaterium ypeb C-terminal domain
5BOI · Germination protein ypeb: “Bacillus megaterium ypeb C-terminal domain”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.49). MolNFT v1 #114406 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BOI
- Type
- protein
- Length
- 226 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germination protein ypeb
- UniProt
- D5DRI0
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Germination protein ypeb | protein | 226 | 16% helix, 44% strand | D5DRI0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.49 | 0.77 | 27 | empty |
| 2 | 53 | 0.31 | 0.76 | 13 | empty |
| 3 | 59 | 0.29 | 0.74 | 13 | empty |
| 4 | 57 | 0.27 | 0.73 | 15 | empty |
Compared structures
- 5BOI · Bacillus megaterium YpeB C-terminal domain · 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 D5DRI0
- Elsewhere: RCSB PDB 5BOI · PDBe 5BOI · UniProt D5DRI0
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