Research workbench
Crystal structure of the lectin I from ulex europaeus in complex with the methyl glycoside of alpha-L-fucose
Analyse Crystal structure of the lectin I from ulex europaeus in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JXN
- Type
- protein
- Length
- 959 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-H(O) lectin I
- UniProt
- P22972
- Ligands
- MFU, MN, CA
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Anti-H(O) lectin I | protein | 240 | 5% helix, 45% strand | P22972 |
| D | Anti-H(O) lectin I | protein | 239 | 6% helix, 45% strand | P22972 |
Ligands and binding sites
- MFU · methyl alpha-L-fucopyranoside · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains C
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 | 106 | 0.47 | 0.80 | 26 | empty |
| 2 | 90 | 0.44 | 0.80 | 22 | empty |
| 3 | 83 | 0.43 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1000 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 969 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 87 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1JXN · Crystal Structure of the Lectin I from Ulex europaeus in complex with the methyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P22972 · AlphaFold monomer V2.0 prediction for anti-H(O) lectin 1 (P22972) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P22972
- Elsewhere: RCSB PDB 1JXN · PDBe 1JXN · UniProt P22972
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