Research workbench
Crystal structure of yvdt from bacillus subtilis
Analyse Crystal structure of yvdt from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F07
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yvdt
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yvdt | protein | 197 | 72% helix, 1% strand | — |
| B | Yvdt | protein | 196 | 72% helix, 1% strand | — |
Ligands and binding sites
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.87 | 0.96 | 48 | BTB |
| 2 | 154 | 0.48 | 0.77 | 26 | empty |
| 3 | 95 | 0.42 | 0.78 | 17 | empty |
| 4 | 51 | 0.27 | 0.74 | 8 | empty |
Interfaces
1 interface between chains.
- A–B · 1635 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2F07 · Crystal Structure of YvdT from Bacillus subtilis · 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
- Elsewhere: RCSB PDB 2F07 · PDBe 2F07
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