Research workbench
Crystal structure of snake gourd (trichosanthes anguina) seed lectin, a three chain homologue of type II rips
Analyse Crystal structure of snake gourd (trichosanthes anguina) seed lectin, a three… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HR6
- Type
- protein
- Length
- 511 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- Ligands
- AMG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin | protein | 41 | 37% helix, 34% strand | — |
| B | Lectin | protein | 206 | 41% helix, 24% strand | — |
| C | Lectin | protein | 264 | 11% helix, 40% strand | — |
Ligands and binding sites
- AMG · methyl alpha-D-galactopyranoside · ligand · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.79 | 0.97 | 23 | empty |
| 2 | 329 | 0.57 | 0.76 | 37 | empty |
| 3 | 259 | 0.57 | 0.78 | 34 | empty |
| 4 | 118 | 0.43 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1765 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1757 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 155 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4HR6 · Crystal structure of snake gourd (Trichosanthes anguina) seed lectin, a three chain… · 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
- Elsewhere: RCSB PDB 4HR6 · PDBe 4HR6
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