Research workbench
Crystal structures of novel monomeric monocot mannose- binding lectins from gastrodia elata
Analyse Crystal structures of novel monomeric monocot mannose- binding lectins from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XD5
- Type
- protein
- Length
- 445 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antifungal protein gafp-1
- UniProt
- Q9AXZ2
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Antifungal protein gafp-1 | protein | 112 | 0% helix, 46% strand | Q9AXZ2 |
| C | Antifungal protein gafp-1 | protein | 111 | 0% helix, 47% strand | Q9AXZ2 |
| D | Antifungal protein gafp-1 | protein | 110 | 0% helix, 47% strand | Q9AXZ2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.42 | 0.79 | 26 | empty |
| 2 | 66 | 0.30 | 0.74 | 14 | empty |
| 3 | 60 | 0.30 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 583 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 555 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 273 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1XD5 · Crystal structures of novel monomeric monocot mannose-binding lectins from Gastrodia elata · 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
- Every structure of UniProt Q9AXZ2
- Elsewhere: RCSB PDB 1XD5 · PDBe 1XD5 · UniProt Q9AXZ2
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