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Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers complexes with N-acetyl-D-glucosamine
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
- 1IPJ
- Type
- protein
- Length
- 1,088 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-conglycinin, beta chain
- UniProt
- P25974
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-conglycinin, beta chain | protein | 357 | 16% helix, 43% strand | P25974 |
| B | Beta-conglycinin, beta chain | protein | 363 | 18% helix, 41% strand | P25974 |
| C | Beta-conglycinin, beta chain | protein | 368 | 18% helix, 40% strand | P25974 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.61 | 0.75 | 55 | empty |
| 2 | 178 | 0.59 | 0.81 | 33 | empty |
| 3 | 332 | 0.56 | 0.76 | 42 | empty |
| 4 | 165 | 0.54 | 0.80 | 27 | empty |
| 5 | 191 | 0.50 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2599 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2450 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2434 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 1IPJ · 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 A against A, TM-score 0.99
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 1IPJ · PDBe 1IPJ · UniProt P25974
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