MolNFT v1 · #152168 · protein
Crystal structure of encapsulin from mycolicibacterium hassiacum
6I9G · Linocin-M18: “Crystal structure of encapsulin from mycolicibacterium hassiacum”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.59). MolNFT v1 #152168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6I9G
- Type
- protein
- Length
- 3,975 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linocin-M18
- EC
- 3.4.-.-
- UniProt
- K5BEG2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Linocin-M18 (EC 3.4.-.-) | protein | 265 | 36% helix, 32% strand | K5BEG2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 117 copies · chains A, L, M, N, O, B, C, D, E, F, G, H, I, J, K
- GOL · Glycerol · additive · 4 copies · chains C, D, B, F, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.59 | 0.85 | 28 | SO4 |
| 2 | 138 | 0.57 | 0.83 | 23 | SO4 |
| 3 | 170 | 0.55 | 0.81 | 30 | SO4 |
| 4 | 210 | 0.54 | 0.78 | 30 | SO4 |
| 5 | 181 | 0.54 | 0.79 | 32 | SO4 |
Interfaces
24 interfaces between chains.
- F–G · 1425 Ų buried · 28 hydrogen bonds · protein-protein
- H–M · 1411 Ų buried · 25 hydrogen bonds · protein-protein
- E–N · 1404 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1360 Ų buried · 17 hydrogen bonds · protein-protein
- G–K · 1356 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6I9G · Crystal structure of encapsulin from Mycolicibacterium hassiacum · 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 K5BEG2
- Elsewhere: RCSB PDB 6I9G · PDBe 6I9G · UniProt K5BEG2
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