MolNFT v1 · #69122 · protein
Crystal structure of procruciferin, 11S globulin from brassica napus
3KGL: “Crystal structure of procruciferin, 11S globulin from brassica napus”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.80). MolNFT v1 #69122 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KGL
- Type
- protein
- Length
- 2,347 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cruciferin
- UniProt
- Q7XB53
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cruciferin | protein | 398 | 13% helix, 39% strand | Q7XB53 |
| B | Cruciferin | protein | 387 | 13% helix, 37% strand | Q7XB53 |
| C | Cruciferin | protein | 387 | 12% helix, 37% strand | Q7XB53 |
| D | Cruciferin | protein | 390 | 12% helix, 38% strand | Q7XB53 |
| E | Cruciferin | protein | 389 | 13% helix, 37% strand | Q7XB53 |
| F | Cruciferin | protein | 396 | 13% helix, 38% strand | Q7XB53 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D, F, E
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.80 | 0.84 | 80 | empty |
| 2 | 222 | 0.79 | 0.93 | 31 | empty |
| 3 | 238 | 0.78 | 0.92 | 48 | empty |
| 4 | 328 | 0.77 | 0.89 | 53 | SO4 |
| 5 | 165 | 0.76 | 0.93 | 32 | empty |
Interfaces
12 interfaces between chains.
- D–E · 2956 Ų buried · 62 hydrogen bonds · protein-protein
- E–F · 2956 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 2926 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 2917 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2910 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3KGL · Crystal structure of procruciferin, 11S globulin from Brassica napus · 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 Q7XB53
- Elsewhere: RCSB PDB 3KGL · PDBe 3KGL · UniProt Q7XB53
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