MolNFT v1 · #141170 · protein
Structure of major royal jelly protein 1 oligomer
5YYL: “Structure of major royal jelly protein 1 oligomer”. X-ray diffraction, 2 ligands (94R, NAG), 11 pockets (best druggability 0.79). MolNFT v1 #141170 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YYL
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major royal jelly protein 1; Apisimin
- UniProt
- O18330, Q8ISL8
- Ligands
- 94R, NAG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major royal jelly protein 1 | protein | 405 | 12% helix, 41% strand | O18330 |
| B | Major royal jelly protein 1 | protein | 375 | 9% helix, 39% strand | O18330 |
| C | Apisimin | protein | 41 | 76% helix, 0% strand | Q8ISL8 |
| D | Apisimin | protein | 43 | 72% helix, 0% strand | Q8ISL8 |
Ligands and binding sites
- 94R · (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.79 | 0.81 | 91 | empty |
| 2 | 719 | 0.79 | 0.83 | 79 | empty |
| 3 | 982 | 0.77 | 0.78 | 50 | 94R |
| 4 | 204 | 0.77 | 0.92 | 46 | empty |
| 5 | 780 | 0.76 | 0.81 | 89 | empty |
Interfaces
5 interfaces between chains.
- A–B · 841 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 426 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 418 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 308 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5YYL · Structure of Major Royal Jelly Protein 1 Oligomer · the same entry in another collection · chain D against D, TM-score 1.00
- O18330 · AlphaFold monomer V2.0 prediction for major royal jelly protein 1 (O18330) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q8ISL8 · AlphaFold monomer V2.0 prediction for apisimin (Q8ISL8) · a predicted model of the same protein · chain D against A, TM-score 0.60
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 O18330
- Every structure of UniProt Q8ISL8
- Elsewhere: RCSB PDB 5YYL · PDBe 5YYL · UniProt O18330 · UniProt Q8ISL8
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