Research workbench
Crystal structure of lp-46/N44
Analyse Crystal structure of lp-46/N44 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YC0
- Type
- protein
- Length
- 433 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; Lp-46
- UniProt
- Q1HMR5
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Envelope glycoprotein | protein | 42 | 95% helix, 0% strand | Q1HMR5 |
| B | Envelope glycoprotein | protein | 44 | 95% helix, 0% strand | Q1HMR5 |
| C, F | Envelope glycoprotein | protein | 43 | 95% helix, 0% strand | Q1HMR5 |
| Q, W, I | Lp-46 | protein | 29 | 93% helix, 0% strand | — |
| P, G | Lp-46 | protein | 31 | 94% helix, 0% strand | — |
| H | Lp-46 | protein | 28 | 93% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.74 | 0.79 | 57 | empty |
| 2 | 108 | 0.43 | 0.78 | 23 | empty |
| 3 | 114 | 0.40 | 0.75 | 15 | empty |
| 4 | 112 | 0.39 | 0.75 | 18 | empty |
| 5 | 68 | 0.33 | 0.75 | 8 | empty |
Interfaces
22 interfaces between chains.
- C–Q · 837 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 810 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 808 Ų buried · 5 hydrogen bonds · protein-protein
- A–W · 791 Ų buried · 5 hydrogen bonds · protein-protein
- D–I · 790 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5YC0 · Crystal structure of LP-46/N44 · 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 Q1HMR5
- Elsewhere: RCSB PDB 5YC0 · PDBe 5YC0 · UniProt Q1HMR5
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