Research workbench
Crystal structure of the S111A mutant of member of mccf clade from listeria monocytogenes egd-E with product
Analyse Crystal structure of the S111A mutant of member of mccf clade from listeria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4INJ
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO1638 protein
- UniProt
- Q8Y6P6
- Ligands
- LMS, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | LMO1638 protein | protein | 326 | 32% helix, 22% strand | Q8Y6P6 |
Ligands and binding sites
- LMS · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl sulfamate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.83 | 0.83 | 88 | LMS, MG, GOL |
| 2 | 50 | 0.53 | 0.89 | 20 | empty |
| 3 | 169 | 0.46 | 0.75 | 20 | empty |
| 4 | 135 | 0.45 | 0.76 | 21 | empty |
| 5 | 54 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1600 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4INJ · Crystal structure of the S111A mutant of member of MccF clade from Listeria monocytogenes… · 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 Q8Y6P6
- Elsewhere: RCSB PDB 4INJ · PDBe 4INJ · UniProt Q8Y6P6
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