MolNFT v1 · #117618 · protein
Crystal structure of an S-component of ecf transporter
5EDL · Putative HMP/THIAMINE permease protein ykoe: “Crystal structure of an S-component of ecf transporter”. X-ray diffraction, 2 ligands (MPG, VIB), 1 pocket (best druggability 0.66). MolNFT v1 #117618 on GenesisL1: 3D structure, binding…
- PDB
- 5EDL
- Type
- protein
- Length
- 197 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative HMP/THIAMINE permease protein ykoe
- UniProt
- O34738
- Ligands
- MPG, VIB
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative HMP/THIAMINE permease protein ykoe | protein | 197 | 80% helix, 0% strand | O34738 |
Ligands and binding sites
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 2 copies · chains A
- VIB · 3-(4-amino-2-methyl-pyrimidin-5-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium · ligand · 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 | 219 | 0.66 | 0.84 | 24 | VIB |
Compared structures
- 5EDL · Crystal structure of an S-component of ECF transporter · the same entry in another collection · chain A against A, TM-score 1.00
- O34738 · AlphaFold monomer V2.0 prediction for putative HMP/THIAMINE permease protein ykoe (O34738) · 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 O34738
- Elsewhere: RCSB PDB 5EDL · PDBe 5EDL · UniProt O34738
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