Research workbench
Crystal structure of banana lectin H84T bound to dimannose
Analyse Crystal structure of banana lectin H84T bound to dimannose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PIT
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ripening-associated protein
- UniProt
- O22321
- Ligands
- MAN
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 69% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ripening-associated protein | protein | 140 | 0% helix, 70% strand | O22321 |
| B | Ripening-associated protein | protein | 144 | 0% helix, 67% strand | O22321 |
| C | Ripening-associated protein | protein | 141 | 0% helix, 71% strand | O22321 |
| D | Ripening-associated protein | protein | 143 | 0% helix, 67% strand | O22321 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.77 | 0.82 | 60 | GOL |
| 2 | 114 | 0.46 | 0.79 | 17 | GOL |
| 3 | 103 | 0.43 | 0.78 | 20 | GOL |
| 4 | 53 | 0.24 | 0.72 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 805 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 777 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 499 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 321 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4PIT · Crystal Structure of Banana Lectin H84T bound to dimannose · 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 O22321
- Elsewhere: RCSB PDB 4PIT · PDBe 4PIT · UniProt O22321
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