Research workbench
Crystal structure of wild-type yabj protein from bacillus subtilis (natto).
Analyse Crystal structure of wild-type yabj protein from bacillus subtilis (natto). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y6U
- Type
- protein
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yabj protein
- UniProt
- D4G3D4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Yabj protein | protein | 124 | 31% helix, 30% strand | D4G3D4 |
Ligands and binding sites
- ACY · Acetic acid · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.80 | 0.98 | 27 | empty |
| 2 | 163 | 0.63 | 0.84 | 23 | empty |
| 3 | 207 | 0.63 | 0.83 | 27 | empty |
| 4 | 220 | 0.61 | 0.81 | 28 | ACY |
| 5 | 79 | 0.55 | 0.86 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 953 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 947 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 940 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5Y6U · Crystal structure of wild-type YabJ protein from Bacillus subtilis (natto). · 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 D4G3D4
- Elsewhere: RCSB PDB 5Y6U · PDBe 5Y6U · UniProt D4G3D4
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