Research workbench
Crystal structure of eal-like domain protein ydiv
Analyse Crystal structure of eal-like domain protein ydiv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TLQ
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein ydiv
- UniProt
- P76204
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein ydiv | protein | 236 | 44% helix, 22% strand | P76204 |
| B | Regulatory protein ydiv | protein | 235 | 44% helix, 23% strand | P76204 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.63 | 0.84 | 26 | empty |
| 2 | 260 | 0.56 | 0.77 | 40 | PO4 |
| 3 | 301 | 0.56 | 0.76 | 42 | PO4, GOL |
| 4 | 112 | 0.48 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 581 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3TLQ · Crystal structure of EAL-like domain protein YdiV · the same entry in another collection · chain A against A, TM-score 1.00
- P76204 · AlphaFold monomer V2.0 prediction for putative anti-FLHC(2)FLHD(4) factor ydiv (P76204) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P76204
- Elsewhere: RCSB PDB 3TLQ · PDBe 3TLQ · UniProt P76204
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