Research workbench
Crystal structure of the YML079W protein from saccharomyces cerevisiae reveals a new sequence family of the jelly roll fold.
Analyse Crystal structure of the YML079W protein from saccharomyces cerevisiae reveals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XE8
- Type
- protein
- Length
- 570 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 22.5 kda protein in TUB1-CPR3 intergenic region
- UniProt
- Q03629
- Ligands
- ADE
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical 22.5 kda protein in TUB1-CPR3 intergenic region | protein | 189 | 21% helix, 43% strand | Q03629 |
| B | Hypothetical 22.5 kda protein in TUB1-CPR3 intergenic region | protein | 193 | 15% helix, 40% strand | Q03629 |
| C | Hypothetical 22.5 kda protein in TUB1-CPR3 intergenic region | protein | 188 | 20% helix, 41% strand | Q03629 |
Ligands and binding sites
- ADE · Adenine · ligand · chains A
- CIT · Citric acid · additive · chains A, B
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.67 | 0.93 | 21 | ADE |
| 2 | 119 | 0.66 | 0.89 | 21 | GOL |
| 3 | 115 | 0.62 | 0.87 | 20 | empty |
| 4 | 253 | 0.55 | 0.77 | 28 | empty |
| 5 | 250 | 0.47 | 0.73 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1393 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 297 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1XE8 · Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new… · the same entry in another collection · chain A against A, TM-score 1.00
- Q03629 · AlphaFold monomer V2.0 prediction for uncharacterized protein YML079W (Q03629) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q03629
- Elsewhere: RCSB PDB 1XE8 · PDBe 1XE8 · UniProt Q03629
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