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Crystal structure of conglutin gamma, a unique basic 7S globulin from lupine seeds
Analyse Crystal structure of conglutin gamma, a unique basic 7S globulin from lupine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PPH
- Type
- protein
- Length
- 2,348 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conglutin gamma
- UniProt
- Q42369
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conglutin gamma | protein | 390 | 17% helix, 38% strand | Q42369 |
| B, E | Conglutin gamma | protein | 391 | 15% helix, 38% strand | Q42369 |
| C | Conglutin gamma | protein | 392 | 15% helix, 39% strand | Q42369 |
| D | Conglutin gamma | protein | 392 | 16% helix, 40% strand | Q42369 |
| F | Conglutin gamma | protein | 392 | 15% helix, 39% strand | Q42369 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, F, B, C, D
- FUC · alpha-L-fucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.81 | 0.83 | 146 | EDO |
| 2 | 1187 | 0.79 | 0.81 | 127 | EDO |
| 3 | 884 | 0.76 | 0.80 | 84 | EDO |
| 4 | 79 | 0.67 | 0.93 | 18 | EDO |
| 5 | 159 | 0.67 | 0.88 | 29 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1342 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1325 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1324 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 726 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 696 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4PPH · Crystal structure of conglutin gamma, a unique basic 7S globulin from lupine seeds · the same entry in another collection · chain F against F, TM-score 1.00
- Q42369 · AlphaFold monomer V2.0 prediction for gamma conglutin 1 (Q42369) · a predicted model of the same protein · chain C 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 Q42369
- Elsewhere: RCSB PDB 4PPH · PDBe 4PPH · UniProt Q42369
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