MolNFT v1 · #27904 · protein
Structure of a mannose-specific jacalin-related lectin from morus nigra in complex with mannose
1XXR · Mannose-binding lectin: “Structure of a mannose-specific jacalin-related lectin from morus nigra in complex with mannose”. X-ray diffraction, 2 ligands (MAN, SO4), 8 pockets (best druggability 0.82). MolNFT v1 #27904 on GenesisL1…
- PDB
- 1XXR
- 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
- MAN, SO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mannose-binding lectin | protein | 154 | 2% helix, 59% strand | Q8LGR3 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B, C, D
- SO4 · Sulfate ion · ion · chains B
- ACY · Acetic acid · additive · 3 copies · chains A, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.82 | 0.92 | 57 | empty |
| 2 | 117 | 0.39 | 0.75 | 27 | empty |
| 3 | 90 | 0.32 | 0.73 | 20 | empty |
| 4 | 69 | 0.30 | 0.74 | 18 | empty |
| 5 | 65 | 0.29 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1146 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 971 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 968 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 123 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1XXR · Structure of a mannose-specific jacalin-related lectin from Morus Nigra in complex with… · 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 1XXR · PDBe 1XXR · UniProt Q8LGR3
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