Research workbench
The crystal structure of the orthorhombic form of the putative had- hydrolase yfnb from bacillus subtilis bound to magnesium reveals interdomain movement
Analyse The crystal structure of the orthorhombic form of the putative had- hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I76
- Type
- protein
- Length
- 680 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative had-hydrolase yfnb
- UniProt
- O06480
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative had-hydrolase yfnb | protein | 223 | 53% helix, 13% strand | O06480 |
| B | Putative had-hydrolase yfnb | protein | 229 | 52% helix, 13% strand | O06480 |
| C | Putative had-hydrolase yfnb | protein | 228 | 50% helix, 14% strand | O06480 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.77 | 0.79 | 103 | MG, CL |
| 2 | 395 | 0.72 | 0.84 | 41 | MG, CL, GOL |
| 3 | 688 | 0.72 | 0.79 | 56 | MG, CL |
| 4 | 94 | 0.32 | 0.73 | 17 | empty |
| 5 | 67 | 0.29 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 620 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 260 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 79 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3I76 · The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from… · the same entry in another collection · chain A against A, TM-score 1.00
- O06480 · AlphaFold monomer V2.0 prediction for putative had-hydrolase yfnb (O06480) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O06480
- Elsewhere: RCSB PDB 3I76 · PDBe 3I76 · UniProt O06480
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