MolNFT v1 · #60743 · protein
Crystal structure of yflh protein from bacillus subtilis. northeast structural genomics consortium target SR326
3D0W: “Crystal structure of yflh protein from bacillus subtilis. northeast structural genomics consortium target…”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #60743 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3D0W
- Type
- protein
- Length
- 341 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yflh protein
- UniProt
- O34306
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Yflh protein | protein | 86 | 73% helix, 0% strand | O34306 |
| C | Yflh protein | protein | 84 | 77% helix, 0% strand | O34306 |
| D | Yflh protein | protein | 85 | 75% helix, 0% strand | O34306 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.63 | 0.82 | 29 | empty |
| 2 | 288 | 0.57 | 0.77 | 29 | empty |
| 3 | 125 | 0.42 | 0.76 | 14 | empty |
| 4 | 52 | 0.30 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1412 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1371 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 362 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3D0W · Crystal structure of YflH protein from Bacillus subtilis. Northeast Structural Genomics… · the same entry in another collection · chain C against C, TM-score 1.00
- O34306 · AlphaFold monomer V2.0 prediction for uncharacterized protein yflh (O34306) · a predicted model of the same protein · chain C against A, TM-score 0.78
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 O34306
- Elsewhere: RCSB PDB 3D0W · PDBe 3D0W · UniProt O34306
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