Research workbench
Cryoem structure of the YEJM/LAPB complex
Analyse Cryoem structure of the YEJM/LAPB complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T6D
- Type
- protein
- Length
- 1,181 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide assembly protein B; Inner membrane protein yejm
- UniProt
- C3TC27, C3T3G2
- Ligands
- LPP, PGV
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 75% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide assembly protein B | protein | 389 | 74% helix, 3% strand | C3TC27 |
| B | Lipopolysaccharide assembly protein B | protein | 381 | 70% helix, 3% strand | C3TC27 |
| C | Inner membrane protein yejm | protein | 213 | 79% helix, 0% strand | C3T3G2 |
| D | Inner membrane protein yejm | protein | 198 | 82% helix, 0% strand | C3T3G2 |
Ligands and binding sites
- LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · chains A, C
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.80 | 0.81 | 73 | LPP |
| 2 | 590 | 0.73 | 0.80 | 44 | empty |
| 3 | 79 | 0.68 | 0.93 | 21 | empty |
| 4 | 820 | 0.66 | 0.74 | 87 | empty |
| 5 | 300 | 0.66 | 0.81 | 45 | PGV |
Interfaces
5 interfaces between chains.
- A–B · 1844 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 700 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 612 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 286 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7T6D · CryoEM structure of the YejM/LapB complex · 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 C3TC27
- Every structure of UniProt C3T3G2
- Elsewhere: RCSB PDB 7T6D · PDBe 7T6D · UniProt C3TC27 · UniProt C3T3G2
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