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Crystal structure of UTR4 protein (unknown transcript 4 protein) (YEL038W) from saccharomyces cerevisiae at 2.28 a resolution
Analyse Crystal structure of UTR4 protein (unknown transcript 4 protein) (YEL038W) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G80
- Type
- protein
- Length
- 894 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein UTR4
- UniProt
- P32626
- Ligands
- MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein UTR4 | protein | 225 | 46% helix, 12% strand | P32626 |
| B, C | Protein UTR4 | protein | 224 | 46% helix, 13% strand | P32626 |
| D | Protein UTR4 | protein | 221 | 45% helix, 13% strand | P32626 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.80 | 0.82 | 84 | MG |
| 2 | 549 | 0.79 | 0.85 | 49 | empty |
| 3 | 543 | 0.72 | 0.81 | 60 | GOL |
| 4 | 445 | 0.66 | 0.78 | 47 | MG |
| 5 | 212 | 0.56 | 0.79 | 28 | PE4 |
Interfaces
3 interfaces between chains.
- A–B · 702 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 684 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 646 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2G80 · Crystal structure of UTR4 protein (Unknown transcript 4 protein) (yel038w) from… · the same entry in another collection · chain D against D, TM-score 1.00
- P32626 · AlphaFold monomer V2.0 prediction for enolase-phosphatase E1 (P32626) · a predicted model of the same protein · chain D 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 P32626
- Elsewhere: RCSB PDB 2G80 · PDBe 2G80 · UniProt P32626
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