Research workbench
Crystal structure of spatholobus parviflorus seed lectin
Analyse Crystal structure of spatholobus parviflorus seed lectin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IPV
- Type
- protein
- Length
- 976 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin alpha chain; Lectin beta chain
- Ligands
- CA, MN
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lectin alpha chain | protein | 249 | 7% helix, 43% strand | — |
| B, D | Lectin beta chain | protein | 239 | 5% helix, 45% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.83 | 0.86 | 82 | empty |
| 2 | 641 | 0.81 | 0.86 | 65 | empty |
| 3 | 342 | 0.72 | 0.84 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 992 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 990 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 984 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 983 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 62 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3IPV · Crystal structure of Spatholobus parviflorus seed lectin · 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 3IPV · PDBe 3IPV
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