MolNFT v1 · #13804 · protein
Interaction of a legume lectin with two components of the bacterial cell wall
1LOD · Legume isolectin I (alpha chain): “Interaction of a legume lectin with two components of the bacterial cell wall”. X-ray diffraction, 3 ligands (MUR, CA, MN), 7 pockets (best druggability 0.73). MolNFT v1 #13804 on GenesisL1: 3D…
- PDB
- 1LOD
- Type
- protein
- Length
- 908 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legume isolectin I (alpha chain); Legume isolectin I (beta chain)
- UniProt
- P04122, P12306
- Ligands
- MUR, CA, MN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Legume isolectin I (alpha chain) | protein | 180 | 2% helix, 45% strand | P04122 |
| B, F | Legume isolectin I (beta chain) | protein | 47 | 6% helix, 64% strand | P12306 |
| D, H | Legume isolectin I (beta chain) | protein | 47 | 9% helix, 62% strand | P12306 |
Ligands and binding sites
- MUR · beta-muramic acid · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 4 copies · chains A, C, E, G
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.73 | 0.77 | 84 | empty |
| 2 | 75 | 0.47 | 0.83 | 19 | empty |
| 3 | 122 | 0.45 | 0.78 | 19 | empty |
| 4 | 110 | 0.43 | 0.78 | 19 | empty |
| 5 | 54 | 0.34 | 0.79 | 19 | empty |
Interfaces
14 interfaces between chains.
- E–F · 3936 Ų buried · 94 hydrogen bonds · protein-protein
- G–H · 3919 Ų buried · 98 hydrogen bonds · protein-protein
- A–B · 3908 Ų buried · 94 hydrogen bonds · protein-protein
- C–D · 3889 Ų buried · 98 hydrogen bonds · protein-protein
- A–C · 852 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1LOD · Interaction of a legume lectin with two components of the bacterial cell wall · the same entry in another collection · chain H against H, TM-score 1.00
- P04122 · AlphaFold monomer V2.0 prediction for lectin beta-1 and beta-2 chains (P04122) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P12306 · AlphaFold monomer V2.0 prediction for MANNOSE/GLUCOSE-specific lectin alpha 1 chain… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P04122
- Every structure of UniProt P12306
- Elsewhere: RCSB PDB 1LOD · PDBe 1LOD · UniProt P04122 · UniProt P12306
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