Research workbench
Structure, interactions and evolutionary implications of a domain- swapped lectin dimer from mycobacterium smegmatis
Analyse Structure, interactions and evolutionary implications of a domain- swapped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OIZ
- Type
- protein
- Length
- 532 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysm domain protein
- UniProt
- A0QYH7
- Ligands
- MMA
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lysm domain protein | protein | 107 | 0% helix, 48% strand | A0QYH7 |
| D | Lysm domain protein | protein | 106 | 0% helix, 47% strand | A0QYH7 |
| E | Lysm domain protein | protein | 105 | 0% helix, 38% strand | A0QYH7 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 6 copies · chains B, C, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.53 | 0.74 | 40 | empty |
| 2 | 222 | 0.50 | 0.76 | 33 | MMA |
| 3 | 174 | 0.46 | 0.75 | 34 | MMA |
| 4 | 119 | 0.45 | 0.78 | 32 | MMA |
Interfaces
7 interfaces between chains.
- A–B · 2484 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2475 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 501 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 152 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OIZ · 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 4OIZ · PDBe 4OIZ · UniProt A0QYH7
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