Research workbench
Improved structure of phytohemagglutinin-L from the kidney bean
Analyse Improved structure of phytohemagglutinin-L from the kidney bean in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G8W
- Type
- protein
- Length
- 932 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucoagglutinating phytohemagglutinin
- UniProt
- P05087
- Ligands
- NAG, MN, CA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Leucoagglutinating phytohemagglutinin | protein | 233 | 4% helix, 46% strand | P05087 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.69 | 0.76 | 68 | empty |
| 2 | 757 | 0.68 | 0.76 | 59 | empty |
| 3 | 97 | 0.59 | 0.86 | 24 | empty |
| 4 | 98 | 0.56 | 0.85 | 31 | empty |
| 5 | 58 | 0.28 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 856 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 832 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 675 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 671 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 1G8W · Improved structure of phytohemagglutinin-L from the kidney bean · the same entry in another collection · chain A against A, TM-score 1.00
- P05087 · AlphaFold monomer V2.0 prediction for leucoagglutinating phytohemagglutinin (P05087) · 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 P05087
- Elsewhere: RCSB PDB 1G8W · PDBe 1G8W · UniProt P05087
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