MolNFT v1 · #102340 · protein
Structure, interactions and evolutionary implications of a domain- swapped lectin dimer from mycobacterium smegmatis
4OIT · Lysm domain protein: “Structure, interactions and evolutionary implications of a domain- swapped lectin dimer from mycobacterium…”. X-ray diffraction, 2 ligands (MAN, BMA), 5 pockets (best druggability 0.56). MolNFT v1 #102340 on…
- PDB
- 4OIT
- Type
- protein
- Length
- 425 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysm domain protein
- UniProt
- A0QYH7
- Ligands
- MAN, BMA
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Lysm domain protein | protein | 106 | 0% helix, 52% strand | A0QYH7 |
| B | Lysm domain protein | protein | 107 | 0% helix, 50% strand | A0QYH7 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.56 | 0.79 | 41 | empty |
| 2 | 199 | 0.50 | 0.76 | 29 | empty |
| 3 | 171 | 0.45 | 0.75 | 29 | empty |
| 4 | 53 | 0.35 | 0.79 | 15 | MAN |
| 5 | 55 | 0.32 | 0.77 | 16 | MAN |
Interfaces
6 interfaces between chains.
- A–B · 2470 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2461 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 149 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4OIT · Structure, interactions and evolutionary implications of a domain-swapped lectin dimer… · 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 A0QYH7
- Elsewhere: RCSB PDB 4OIT · PDBe 4OIT · UniProt A0QYH7
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