Research workbench
Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers
Analyse Crystal structures of recombinant and native soybean beta-conglycinin beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IPK
- Type
- protein
- Length
- 1,112 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-conglycinin, beta chain
- UniProt
- P25974
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-conglycinin, beta chain | protein | 368 | 12% helix, 42% strand | P25974 |
| B | Beta-conglycinin, beta chain | protein | 365 | 16% helix, 41% strand | P25974 |
| C | Beta-conglycinin, beta chain | protein | 379 | 18% helix, 42% strand | P25974 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.71 | 0.75 | 129 | empty |
| 2 | 259 | 0.62 | 0.80 | 34 | empty |
| 3 | 185 | 0.50 | 0.77 | 24 | empty |
| 4 | 131 | 0.41 | 0.75 | 17 | empty |
| 5 | 53 | 0.28 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2676 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2581 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2514 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1IPK · Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers · the same entry in another collection · chain A against A, TM-score 1.00
- P25974 · AlphaFold monomer V2.0 prediction for beta-conglycinin beta subunit 1 (P25974) · 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 P25974
- Elsewhere: RCSB PDB 1IPK · PDBe 1IPK · UniProt P25974
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