Research workbench
Crystal structure of bacillus subtilis ymdb, a global regulator of late adaptive responses.
Analyse Crystal structure of bacillus subtilis ymdb, a global regulator of late… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B2O
- Type
- protein
- Length
- 1,056 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ymdb phosphodiesterase
- UniProt
- O31775
- Ligands
- FE2, PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ymdb phosphodiesterase | protein | 264 | 25% helix, 30% strand | O31775 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.77 | 0.98 | 25 | empty |
| 2 | 99 | 0.77 | 0.98 | 24 | empty |
| 3 | 101 | 0.77 | 0.97 | 24 | empty |
| 4 | 96 | 0.77 | 0.97 | 24 | empty |
| 5 | 1022 | 0.74 | 0.77 | 93 | PO4 |
Interfaces
6 interfaces between chains.
- C–D · 1737 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1731 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 530 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 498 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 195 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4B2O · Crystal structure of Bacillus subtilis YmdB, a global regulator of late adaptive… · the same entry in another collection · chain A against A, TM-score 1.00
- O31775 · AlphaFold monomer V2.0 prediction for 2',3'-cyclic-nucleotide 2'-phosphodiesterase… · a predicted model of the same protein · 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 O31775
- Elsewhere: RCSB PDB 4B2O · PDBe 4B2O · UniProt O31775
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