Research workbench
Bombyx mori lipoprotein 7 (crystal form II) at 2.50 a resolution
Analyse Bombyx mori lipoprotein 7 (crystal form II) at 2.50 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EFR
- Type
- protein
- Length
- 939 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 30KDA protein
- UniProt
- E5EVW2
- Ligands
- SCN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 30KDA protein | protein | 235 | 33% helix, 34% strand | E5EVW2 |
| B, D | 30KDA protein | protein | 234 | 32% helix, 33% strand | E5EVW2 |
| C | 30KDA protein | protein | 236 | 31% helix, 34% strand | E5EVW2 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.78 | 0.96 | 27 | empty |
| 2 | 560 | 0.63 | 0.75 | 47 | empty |
| 3 | 285 | 0.61 | 0.79 | 44 | empty |
| 4 | 166 | 0.49 | 0.77 | 23 | empty |
| 5 | 92 | 0.49 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 931 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 730 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4EFR · Bombyx mori lipoprotein 7 (crystal form II) at 2.50 A resolution · 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 E5EVW2
- Elsewhere: RCSB PDB 4EFR · PDBe 4EFR · UniProt E5EVW2
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