Research workbench
EM structure of mpeg-1 (L425K, alpha conformation) soluble pre-pore complex
Analyse EM structure of mpeg-1 (L425K, alpha conformation) soluble pre-pore complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U2K
- Type
- protein
- Length
- 604 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage-expressed gene 1 protein
- UniProt
- Q2M385
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.69
Structure
electron microscopy · 1 distinct chain · 16% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Macrophage-expressed gene 1 protein | protein | 604 | 16% helix, 25% strand | Q2M385 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.69 | 0.80 | 47 | empty |
| 2 | 152 | 0.47 | 0.77 | 23 | empty |
| 3 | 80 | 0.47 | 0.82 | 19 | empty |
| 4 | 145 | 0.45 | 0.76 | 33 | empty |
| 5 | 57 | 0.40 | 0.81 | 13 | empty |
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6U2K · EM structure of MPEG-1 (L425K, alpha conformation) soluble pre-pore complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q2M385 · AlphaFold monomer V2.0 prediction for macrophage-expressed gene 1 protein (Q2M385) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 6U2K · PDBe 6U2K · UniProt Q2M385
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