MolNFT v1 · #90850 · protein
Crystal structure of C-terminal domain of putative periplasmic protein ydgh from S. enterica
4EVU: “Crystal structure of C-terminal domain of putative periplasmic protein ydgh from S. enterica”. X-ray diffraction, 2 ligands (SO4, CL), 1 pocket (best druggability 0.47). MolNFT v1 #90850 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4EVU
- Type
- protein
- Length
- 133 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative periplasmic protein ydgh
- UniProt
- Q8ZPL1
- Ligands
- SO4, CL
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative periplasmic protein ydgh | protein | 65 | 28% helix, 40% strand | Q8ZPL1 |
| B | Putative periplasmic protein ydgh | protein | 68 | 28% helix, 41% strand | Q8ZPL1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.47 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4EVU · Crystal structure of C-terminal domain of putative periplasmic protein ydgH from S.… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8ZPL1
- Elsewhere: RCSB PDB 4EVU · PDBe 4EVU · UniProt Q8ZPL1
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