MolNFT v1 · #81505 · protein
Crystal structure of butea monosperma seed lectin
3USU · Lectin alpha chain: “Crystal structure of butea monosperma seed lectin”. X-ray diffraction, 8 ligands (ABU, NAG, FUC), 13 pockets (best druggability 0.82). MolNFT v1 #81505 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3USU
- Type
- protein
- Length
- 1,968 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin alpha chain; Lectin beta chain
- Ligands
- ABU, NAG, FUC, BMA, MAN, XYP, CA, MN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Lectin alpha chain | protein | 250 | 7% helix, 44% strand | — |
| B, D, F, H | Lectin beta chain | protein | 242 | 5% helix, 46% strand | — |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, H, B, C, E, G, D
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains H
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar
- XYP · beta-D-xylopyranose · sugar
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.82 | 0.89 | 61 | GOL |
| 2 | 536 | 0.82 | 0.88 | 66 | GOL |
| 3 | 485 | 0.81 | 0.88 | 63 | GOL |
| 4 | 542 | 0.81 | 0.87 | 47 | empty |
| 5 | 410 | 0.81 | 0.89 | 52 | GOL |
Interfaces
13 interfaces between chains.
- F–G · 1104 Ų buried · 30 hydrogen bonds · protein-protein
- E–H · 1099 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1043 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1023 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 978 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 3USU · Crystal structure of Butea monosperma seed lectin · 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
- Elsewhere: RCSB PDB 3USU · PDBe 3USU
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