Research workbench
Structure of peptst from coc imisx setup collected by still serial crystallography on crystals prelocated by 2D X-ray phase-contrast imaging
Analyse Structure of peptst from coc imisx setup collected by still serial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YOG
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-or TRIPEPTIDE:H+ symporter
- UniProt
- Q5M4H8
- Ligands
- 78M, PO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-or TRIPEPTIDE:H+ symporter | protein | 448 | 80% helix, 1% strand | Q5M4H8 |
Ligands and binding sites
- 78M · (2S)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 20 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.76 | 0.82 | 45 | empty |
| 2 | 567 | 0.65 | 0.75 | 58 | 78M |
| 3 | 56 | 0.27 | 0.73 | 17 | PGE |
Compared structures
- 6YOG · Structure of PepTSt from COC IMISX setup collected by still serial crystallography on… · 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 Q5M4H8
- Elsewhere: RCSB PDB 6YOG · PDBe 6YOG · UniProt Q5M4H8
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