Research workbench
Structure of a mannose-specific jacalin-related lectin from morus nigra
Analyse Structure of a mannose-specific jacalin-related lectin from morus nigra in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XXQ
- Type
- protein
- Length
- 616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-binding lectin
- UniProt
- Q8LGR3
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mannose-binding lectin | protein | 154 | 0% helix, 59% strand | Q8LGR3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.81 | 0.89 | 67 | empty |
| 2 | 92 | 0.32 | 0.73 | 21 | empty |
| 3 | 82 | 0.31 | 0.73 | 22 | empty |
| 4 | 61 | 0.29 | 0.74 | 17 | empty |
| 5 | 54 | 0.26 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1154 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1125 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 981 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 967 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 124 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1XXQ · Structure of a mannose-specific jacalin-related lectin from Morus nigra · 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 Q8LGR3
- Elsewhere: RCSB PDB 1XXQ · PDBe 1XXQ · UniProt Q8LGR3
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