Research workbench
Interaction of a legume lectin with two components of the bacterial cell wall
Analyse Interaction of a legume lectin with two components of the bacterial cell wall in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LOC
- Type
- protein
- Length
- 914 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legume isolectin I (alpha chain); Legume isolectin I (beta chain); Muramyl-dipeptide…
- UniProt
- P04122, P12306
- Ligands
- MDP, DAL, CA, MN
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Legume isolectin I (alpha chain) | protein | 180 | 3% helix, 45% strand | P04122 |
| B, F | Legume isolectin I (beta chain) | protein | 47 | 9% helix, 64% strand | P12306 |
| 1, 3, 4 | Muramyl-dipeptide D-ala-D-igln | protein | 2 | 0% helix, 0% strand | — |
| D, H | Legume isolectin I (beta chain) | protein | 47 | 6% helix, 62% strand | P12306 |
Ligands and binding sites
- MDP · N-carboxyl-N-methyl-beta-muramic acid · ligand · 4 copies · chains A, B, 1, C, D, E, F, 3, G, H, 4
- DAL · D-alanine · ligand · chains C
- 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.66 | 0.79 | 59 | empty |
| 2 | 422 | 0.59 | 0.75 | 30 | empty |
| 3 | 90 | 0.47 | 0.81 | 18 | empty |
| 4 | 96 | 0.43 | 0.79 | 19 | empty |
| 5 | 50 | 0.38 | 0.81 | 18 | empty |
Interfaces
19 interfaces between chains.
- C–D · 3976 Ų buried · 104 hydrogen bonds · protein-protein
- E–F · 3947 Ų buried · 85 hydrogen bonds · protein-protein
- G–H · 3946 Ų buried · 93 hydrogen bonds · protein-protein
- A–B · 3941 Ų buried · 89 hydrogen bonds · protein-protein
- E–G · 835 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 d-amino, 3 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 1LOC · Interaction of a legume lectin with two components of the bacterial cell wall · the same entry in another collection · chain D against D, 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 G 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 P04122
- Every structure of UniProt P12306
- Elsewhere: RCSB PDB 1LOC · PDBe 1LOC · UniProt P04122 · UniProt P12306
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