Research workbench
2.6 ångström crystal structure of putative yceg-like protein LMO1499 from listeria monocytogenes
Analyse 2.6 ångström crystal structure of putative yceg-like protein LMO1499 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IIW
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO1499 protein
- UniProt
- Q8Y725
- Ligands
- CL, SO4
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LMO1499 protein | protein | 304 | 45% helix, 8% strand | Q8Y725 |
| B | LMO1499 protein | protein | 307 | 46% helix, 7% strand | Q8Y725 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.58 | 0.85 | 28 | empty |
| 2 | 331 | 0.58 | 0.76 | 44 | empty |
| 3 | 278 | 0.58 | 0.78 | 31 | empty |
| 4 | 191 | 0.50 | 0.76 | 27 | empty |
| 5 | 236 | 0.49 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 710 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4IIW · 2.6 Angstrom Crystal Structure of Putative yceG-like Protein lmo1499 from Listeria… · 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 Q8Y725
- Elsewhere: RCSB PDB 4IIW · PDBe 4IIW · UniProt Q8Y725
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