Research workbench
X-ray crystal structure of protein yybh from bacillus subtilis. northeast structural genomics consortium target SR506.
Analyse X-ray crystal structure of protein yybh from bacillus subtilis. northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GXF
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yybh
- UniProt
- P37496
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypothetical protein yybh | protein | 119 | 29% helix, 39% strand | P37496 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.75 | 0.85 | 42 | MES |
| 2 | 384 | 0.74 | 0.84 | 43 | MES |
| 3 | 452 | 0.68 | 0.79 | 41 | MES |
| 4 | 436 | 0.66 | 0.78 | 39 | MES |
| 5 | 308 | 0.58 | 0.77 | 31 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1329 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1317 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 268 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 206 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2GXF · X-Ray Crystal Structure of Protein YybH from Bacillus subtilis. Northeast Structural… · the same entry in another collection · chain A against A, TM-score 1.00
- P37496 · AlphaFold monomer V2.0 prediction for uncharacterized protein yybh (P37496) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P37496
- Elsewhere: RCSB PDB 2GXF · PDBe 2GXF · UniProt P37496
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