Research workbench
Crystal structure of the ygdr protein from E.COLI. northeast structural genomics target ER382A.
Analyse Crystal structure of the ygdr protein from E.COLI. northeast structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FIF
- Type
- protein
- Length
- 452 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized lipoprotein ygdr; Uncharacterized ligand
- UniProt
- P65294
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized lipoprotein ygdr | protein | 55 | 5% helix, 53% strand | P65294 |
| B, F | Uncharacterized lipoprotein ygdr | protein | 56 | 5% helix, 52% strand | P65294 |
| C, D, G | Uncharacterized lipoprotein ygdr | protein | 57 | 5% helix, 56% strand | P65294 |
| E | Uncharacterized lipoprotein ygdr | protein | 52 | 6% helix, 54% strand | P65294 |
| H | Uncharacterized lipoprotein ygdr | protein | 55 | 5% helix, 53% strand | P65294 |
| Y | Uncharacterized ligand | protein | 7 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.61 | 0.78 | 48 | empty |
| 2 | 115 | 0.37 | 0.74 | 23 | empty |
| 3 | 80 | 0.35 | 0.75 | 22 | empty |
| 4 | 118 | 0.34 | 0.72 | 25 | empty |
| 5 | 59 | 0.30 | 0.75 | 14 | empty |
Interfaces
11 interfaces between chains.
- C–D · 359 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 359 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 324 Ų buried · 7 hydrogen bonds · protein-protein
- F–H · 315 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 281 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3FIF · Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P65294 · AlphaFold monomer V2.0 prediction for uncharacterized lipoprotein ygdr (P65294) · a predicted model of the same protein · chain B against A, TM-score 0.79
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 P65294
- Elsewhere: RCSB PDB 3FIF · PDBe 3FIF · UniProt P65294
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