Research workbench
Peptst in complex with hepes (100 mm)
Analyse Peptst in complex with hepes (100 mm) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EIA
- Type
- protein
- Length
- 464 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-or TRIPEPTIDE:H+ symporter
- UniProt
- Q5M4H8
- Ligands
- 78N, 78M, PO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 83% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-or TRIPEPTIDE:H+ symporter | protein | 464 | 83% helix, 1% strand | Q5M4H8 |
Ligands and binding sites
- 78N · (2R)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 13 copies · chains A
- 78M · (2S)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 5 copies · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.79 | 0.83 | 55 | PO4, EPE |
| 2 | 208 | 0.60 | 0.80 | 30 | 78N |
| 3 | 61 | 0.32 | 0.76 | 9 | empty |
| 4 | 71 | 0.31 | 0.74 | 16 | PG4 |
Compared structures
- 6EIA · PepTSt in complex with HEPES (100 mM) · 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 6EIA · PDBe 6EIA · UniProt Q5M4H8
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