Research workbench
Single-particle cryo-EM structure of major facilitator superfamily domain containing 2A in complex with lpc-18:3
Analyse Single-particle cryo-EM structure of major facilitator superfamily domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MJS
- Type
- protein
- Length
- 703 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2AG3 Fab heavy chain; 2AG3 Fab light chain; Major facilitator superfamily domain…
- UniProt
- F1NCD6
- Ligands
- ZGS, NAG
- Pockets
- 3 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 2AG3 Fab heavy chain | protein | 132 | 0% helix, 59% strand | — |
| L | 2AG3 Fab light chain | protein | 113 | 0% helix, 43% strand | — |
| X | Major facilitator superfamily domain containing 2A | protein | 458 | 77% helix, 1% strand | F1NCD6 |
Ligands and binding sites
- ZGS · [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$L^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z}, 15~{Z})-octadeca-9,12,15-trienoate · ligand · chains X
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains X, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.84 | 0.85 | 74 | ZGS |
| 2 | 83 | 0.32 | 0.74 | 21 | empty |
| 3 | 74 | 0.31 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1119 Ų buried · 12 hydrogen bonds · protein-protein
- H–X · 884 Ų buried · 10 hydrogen bonds · protein-protein
- L–X · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7MJS · Single-Particle Cryo-EM Structure of Major Facilitator Superfamily Domain containing 2A… · the same entry in another collection · chain H against H, 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 F1NCD6
- Elsewhere: RCSB PDB 7MJS · PDBe 7MJS · UniProt F1NCD6
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