Research workbench
Crystal structure of a recombinant vatairea macrocarpa seed lectin
Analyse Crystal structure of a recombinant vatairea macrocarpa seed lectin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XXA
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seed lectin
- UniProt
- P81371
- Ligands
- CA, MN
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seed lectin | protein | 234 | 4% helix, 48% strand | P81371 |
| B | Seed lectin | protein | 234 | 4% helix, 47% strand | P81371 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.71 | 0.77 | 82 | empty |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P81371
- Elsewhere: RCSB PDB 4XXA · PDBe 4XXA · UniProt P81371
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