MolNFT v1 · #137773 · protein
Crystal structure of a protein of unknown function YCEH/ECK1052 involved in membrane biogenesis from escherichia COLI
5VYV · UPF0502 protein yceh: “Crystal structure of a protein of unknown function YCEH/ECK1052 involved in membrane biogenesis from…”. X-ray diffraction, 1 pocket (best druggability 0.80). MolNFT v1 #137773 on GenesisL1: 3D structure…
- PDB
- 5VYV
- Type
- protein
- Length
- 343 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0502 protein yceh
- UniProt
- Q8X8M9
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0502 protein yceh | protein | 173 | 42% helix, 10% strand | Q8X8M9 |
| B | UPF0502 protein yceh | protein | 170 | 39% helix, 11% strand | Q8X8M9 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.80 | 0.87 | 62 | PEG |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VYV · Crystal structure of a protein of unknown function YceH/ECK1052 involved in membrane… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X8M9 · AlphaFold monomer V2.0 prediction for UPF0502 protein yceh (Q8X8M9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8X8M9
- Elsewhere: RCSB PDB 5VYV · PDBe 5VYV · UniProt Q8X8M9
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