Research workbench
EM structure of mpeg-1(L425K) pre-pore complex bound to liposome
Analyse EM structure of mpeg-1(L425K) pre-pore complex bound to liposome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U2W
- Type
- protein
- Length
- 8,704 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage-expressed gene 1 protein
- UniProt
- Q2M385
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 19% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Macrophage-expressed gene 1 protein | protein | 544 | 19% helix, 19% strand | Q2M385 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 64 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.87 | 0.90 | 120 | empty |
| 2 | 1100 | 0.86 | 0.87 | 124 | empty |
| 3 | 700 | 0.86 | 0.90 | 102 | empty |
| 4 | 656 | 0.86 | 0.90 | 88 | empty |
| 5 | 513 | 0.83 | 0.90 | 78 | empty |
Interfaces
16 interfaces between chains.
- A–P · 2187 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 2138 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 2129 Ų buried · 11 hydrogen bonds · protein-protein
- N–O · 2115 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 2108 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 112 disulfide, 32 glycan (disulfide, N-glycosylation).
Compared structures
- 6U2W · EM structure of MPEG-1(L425K) pre-pore complex bound to liposome · the same entry in another collection · chain P against P, 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 Q2M385
- Elsewhere: RCSB PDB 6U2W · PDBe 6U2W · UniProt Q2M385
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